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GPL-3 + file LICENSE MD5sum: 8e5fc1c735a447950464f98efcf122dc NeedsCompilation: no File: ADImpute_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: AGDEX Version: 1.54.0 Depends: R (>= 2.10), Biobase, GSEABase Imports: stats License: GPL (>= 2) MD5sum: dc8d55b1bebd8d71b17d69e53c29f41e NeedsCompilation: no File: AGDEX_1.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: AHMassBank Version: 1.6.1 Depends: R (>= 4.2) Imports: AnnotationHubData (>= 1.5.24) Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown, methods, CompoundDb (>= 1.1.4) License: Artistic-2.0 MD5sum: 2c8ae17005e57c006ff8323071bf3380 NeedsCompilation: no File: AHMassBank_1.6.1_R_x86_64-pc-linux-gnu.tar.gz Package: AICcmodavg Version: 2.3-4 Depends: R (>= 3.2.0) Imports: methods, stats, graphics, lattice, MASS, Matrix, nlme, stats4, survival, unmarked, VGAM, xtable Suggests: betareg, coxme, fitdistrplus, glmmTMB, lavaan, lme4, maxlike, nnet, ordinal, pscl, R2jags, R2OpenBUGS, R2WinBUGS, jagsUI, lmerTest License: GPL (>= 2) 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Suggests: testthat, BiocStyle, lintr, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 5dd627f2e257a588d236ffc04b87bef8 NeedsCompilation: no File: ASSIGN_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: ASURAT Version: 1.10.0 Depends: R (>= 4.0.0) Imports: SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp (>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize, grid, grDevices, graphics LinkingTo: Rcpp Suggests: ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi, BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 0ab0f8c1015ba6e5737a5db1f79d1791 NeedsCompilation: yes File: ASURAT_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: ASpli Version: 2.16.0 Depends: methods, grDevices, stats, utils, parallel, edgeR, limma, AnnotationDbi Imports: GenomicRanges, GenomicFeatures, BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle, igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, 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rmarkdown, testthat (>= 3.0.0), tinytest License: Artistic-2.0 MD5sum: 50b4446c6964cabd07bf2da3eb8515ff NeedsCompilation: no File: AnVILBase_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnVILGCP Version: 1.0.0 Imports: AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, parallel, methods, rlang, stats, tibble, tidyr, utils Suggests: AnVIL, BiocStyle, httr2, knitr, rmarkdown, testthat, withr License: Artistic-2.0 MD5sum: 46a193dae46ca6f7b48efbe832dcd1d3 NeedsCompilation: no File: AnVILGCP_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnVILPublish Version: 1.16.0 Imports: AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools, utils, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 3784bca8353f64ebb7c258bcc893e856 NeedsCompilation: no File: AnVILPublish_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnVIL Version: 1.18.5 Depends: R (>= 3.6), dplyr, AnVILBase Imports: stats, utils, methods, futile.logger, jsonlite, httr, rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang, shiny, DT, miniUI, htmltools, BiocManager, BiocBaseUtils Suggests: parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle License: Artistic-2.0 MD5sum: 09b74e2771b9ad531e24fab0c51bb105 NeedsCompilation: no File: AnVIL_1.18.5_R_x86_64-pc-linux-gnu.tar.gz Package: Anaquin Version: 2.30.0 Depends: R (>= 3.3), ggplot2 (>= 2.2.0) Imports: ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils, plyr, DESeq2 Suggests: RUnit, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: dad0148b3109d91cd5f27259f9948e12 NeedsCompilation: no File: Anaquin_2.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: AneuFinderData Version: 1.34.0 Depends: R (>= 3.3) License: file LICENSE MD5sum: 173d60930fb4d51245add188aadfc597 NeedsCompilation: no File: AneuFinderData_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: AneuFinder Version: 1.34.0 Depends: R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData Imports: methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics (>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: Artistic-2.0 MD5sum: aacc2d706961dc004d8f6b05abfd9d84 NeedsCompilation: yes File: AneuFinder_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnnotationDbi Version: 1.68.0 Depends: R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2), Biobase (>= 1.17.0), IRanges Imports: DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST Suggests: utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr License: Artistic-2.0 MD5sum: 00d027b1d57f1da3ae3f425b342234f9 NeedsCompilation: no File: AnnotationDbi_1.68.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnnotationFilter Version: 1.30.0 Depends: R (>= 3.4.0) Imports: utils, methods, GenomicRanges, lazyeval Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown License: Artistic-2.0 MD5sum: 7a88ef945a73450ad3eec99e63677e99 NeedsCompilation: no File: AnnotationFilter_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnnotationForge Version: 1.48.0 Depends: R (>= 3.5.0), methods, utils, BiocGenerics (>= 0.15.10), Biobase (>= 1.17.0), AnnotationDbi (>= 1.33.14) Imports: DBI, RSQLite, XML, S4Vectors, RCurl Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit License: Artistic-2.0 MD5sum: f4608a4a24f7835ea4e820c933479057 NeedsCompilation: no File: AnnotationForge_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: AnnotationHubData Version: 1.36.0 Depends: R (>= 3.2.2), methods, utils, 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CompoundDb, keras, ensembldb, SummarizedExperiment, ExperimentHub, gdsfmt, rmarkdown, HubPub Enhances: AnnotationHubData License: Artistic-2.0 MD5sum: e1d54ecc856a842e50507482d9a70bc8 NeedsCompilation: yes File: AnnotationHub_3.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: AsioHeaders Version: 1.22.1-2 License: BSL-1.0 MD5sum: da548a20aa0cdc6ecd261e72ae83f5e9 NeedsCompilation: no File: AsioHeaders_1.22.1-2_R_x86_64-pc-linux-gnu.tar.gz Package: AssessORF Version: 1.24.0 Depends: R (>= 3.5.0), DECIPHER (>= 2.10.0) Imports: Biostrings, GenomicRanges, IRanges, graphics, grDevices, methods, stats, utils Suggests: AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1) License: GPL-3 MD5sum: 8fe723e1a993140da3fb36bd2700a652 NeedsCompilation: no File: AssessORF_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: AzureAuth Version: 1.3.3 Depends: R (>= 3.3) Imports: utils, httr (>= 1.3), openssl, jsonlite, jose, R6, rappdirs Suggests: knitr, rmarkdown, testthat, httpuv, shiny, shinyjs, AzureRMR, AzureGraph License: MIT + file LICENSE MD5sum: f685360fd71ec45de19ccbcebbd9ee99 NeedsCompilation: no File: AzureAuth_1.3.3_R_x86_64-pc-linux-gnu.tar.gz Package: AzureGraph Version: 1.3.4 Depends: R (>= 3.3) Imports: AzureAuth (>= 1.0.1), utils, httr (>= 1.3), jsonlite, openssl, curl, R6 Suggests: AzureRMR, vctrs, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 08e47cd8e3506bf03c0503720547d0b2 NeedsCompilation: no File: AzureGraph_1.3.4_R_x86_64-pc-linux-gnu.tar.gz Package: AzureRMR Version: 2.4.4 Depends: R (>= 3.3) Imports: AzureGraph (>= 1.2.0), AzureAuth (>= 1.2.1), utils, parallel, httr (>= 1.3), jsonlite, R6, uuid Suggests: knitr, rmarkdown, testthat, httpuv, AzureStor License: MIT + file LICENSE MD5sum: dd61b2c2222f6e45411aee5b42877f5b NeedsCompilation: no File: AzureRMR_2.4.4_R_x86_64-pc-linux-gnu.tar.gz Package: AzureStor Version: 3.7.0 Depends: R (>= 3.3), Imports: utils, R6, httr (>= 1.4.0), mime, openssl, xml2, vctrs, AzureRMR (>= 2.3.0) Suggests: AzureAuth, readr, knitr, rmarkdown, jsonlite, testthat, processx, uuid License: MIT + file LICENSE MD5sum: 0401a7e9631a96749ec1c99da7856b14 NeedsCompilation: no File: AzureStor_3.7.0_R_x86_64-pc-linux-gnu.tar.gz Package: BADER Version: 1.44.0 Suggests: pasilla (>= 0.2.10) License: GPL-2 MD5sum: 4e48f3a0262a042563d1498d4ac4a210 NeedsCompilation: yes File: BADER_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: BAGS Version: 2.46.0 Depends: R (>= 2.10), breastCancerVDX, Biobase License: Artistic-2.0 MD5sum: 5320af25d2e0830bb7104984d66df2e2 NeedsCompilation: yes File: BAGS_2.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: BANDITS Version: 1.22.0 Depends: R (>= 4.3.0) Imports: Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel, foreach, methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, testthat, tximport, BiocStyle, GenomicFeatures, Biostrings License: GPL (>= 3) MD5sum: 9c59804f27aa7b2a6c2b6d34d8d2750d NeedsCompilation: yes File: 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StanHeaders (>= 2.18.0) Suggests: testthat (>= 3.0.0), knitr, rmarkdown License: GPL-3 MD5sum: cc097767349e63c65a28e77fba3a1db8 NeedsCompilation: yes File: BASiCStan_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: BBCAnalyzer Version: 1.36.0 Imports: SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices, GenomicRanges, IRanges, Biostrings Suggests: BSgenome.Hsapiens.UCSC.hg19 License: LGPL-3 MD5sum: 6720225437785a2fbb5313ac75398e60 NeedsCompilation: no File: BBCAnalyzer_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: BB Version: 2019.10-1 Depends: R (>= 2.6.1) Imports: stats, quadprog Suggests: setRNG, survival, Hmisc, numDeriv License: GPL-3 MD5sum: 2b7dde8e7ecc9f35f22957b8f1c1b1b5 NeedsCompilation: no File: BB_2019.10-1_R_x86_64-pc-linux-gnu.tar.gz Package: BBmisc Version: 1.13 Imports: checkmate (>= 1.8.0), data.table, methods, stats, utils Suggests: codetools, microbenchmark, testthat License: BSD_2_clause + file LICENSE MD5sum: e28a94691c7b1d0d60392b621c3031df NeedsCompilation: 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gh, RBGL, graph, rorcid Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, lubridate, networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR, SummarizedExperiment License: MIT + file LICENSE MD5sum: 84d57de71fa7ee1313d0c6a1731616b6 NeedsCompilation: no File: BiocPkgTools_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: BiocSet Version: 1.20.0 Depends: R (>= 3.6), dplyr Imports: methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO, AnnotationDbi, KEGGREST, ontologyIndex, tidyr Suggests: GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache, GO.db, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 3d0835d8b12b91ecd602226729a9b181 NeedsCompilation: no File: BiocSet_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: BiocSingular Version: 1.22.0 Imports: BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray, BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>= 2.21.1) LinkingTo: Rcpp, beachmat, assorthead Suggests: testthat, BiocStyle, knitr, 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shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, MAGeCKFlute, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 685ef6169016367f664f6bd2d4e4fa0a NeedsCompilation: no File: CRISPRball_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: CRISPRseek Version: 1.46.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, GenomeInfoDb, GenomicRanges, dplyr, keras, mltools Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice, MASS, tensorflow, testthat License: GPL (>= 2) MD5sum: 18da27fa20a49a20f2393bc3f335c114 NeedsCompilation: no File: 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gplots, graphics, grid, gtable, knnmi, MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats, SummarizedExperiment Suggests: BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat (>= 3.1.6) License: GPL-3 + file LICENSE MD5sum: 4084d49fd6ec84f7df8e87fa0fb11f86 NeedsCompilation: yes File: CaDrA_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: CaMutQC Version: 1.2.0 Depends: R (>= 4.0.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: c3977fb941cd6ea115da5a0a0098f374 NeedsCompilation: no File: CaMutQC_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: Cairo Version: 1.6-2 Depends: R (>= 2.4.0) Imports: grDevices, graphics Suggests: png Enhances: FastRWeb License: GPL-2 | GPL-3 MD5sum: f20961ed0eac467f1788afefd008108c NeedsCompilation: yes File: Cairo_1.6-2_R_x86_64-pc-linux-gnu.tar.gz Package: CardinalIO Version: 1.4.0 Depends: R (>= 4.4), 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Depends: methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix Imports: utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db License: Artistic-2.0 MD5sum: 93d7658fc27cf6c1821e434ec1267e3e NeedsCompilation: no File: Category_2.72.0_R_x86_64-pc-linux-gnu.tar.gz Package: CatsCradle Version: 1.0.1 Depends: R (>= 4.4.0) Imports: Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma, reshape2, rdist, igraph, geometry, Rfast, data.table, abind, pheatmap, EBImage, S4Vectors, SeuratObject, SingleCellExperiment, SpatialExperiment, Matrix, methods, SummarizedExperiment, msigdbr Suggests: fossil, interp, knitr, BiocStyle, tictoc License: MIT + file LICENSE MD5sum: c87b7980c6eeea0347f76aab39e219c9 NeedsCompilation: no File: CatsCradle_1.0.1_R_x86_64-pc-linux-gnu.tar.gz Package: CausalR Version: 1.38.0 Depends: R 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(>= 3.5.0), RColorBrewer(>= 1.1-2), squash (>= 1.0.8), stats (>= 3.5.0), utils(>= 3.5.0), SummarizedExperiment Suggests: hgu133plus2CellScore, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 7a79f94310d0f0a059c0dff0e1cc3ab2 NeedsCompilation: no File: CellScore_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: CellTrails Version: 1.24.0 Depends: R (>= 3.5), SingleCellExperiment Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats, ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv, reshape2, Rtsne, stats, splines, SummarizedExperiment, utils Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown License: Artistic-2.0 MD5sum: e4f97cfb4d16b7fcfa0c3db28e8ac731 NeedsCompilation: no File: CellTrails_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: CelliD Version: 1.14.0 Depends: R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment Imports: Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater, stringr, irlba, data.table, glue, pbapply, umap, 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BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 15abe43478e8e079a889336fe5a45631 NeedsCompilation: no File: ChIPanalyser_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: ChIPexoQualExample Version: 1.30.0 Depends: R (>= 3.3) Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 238ba41c53a6fff46d34a997e98c7457 NeedsCompilation: no File: ChIPexoQualExample_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: ChIPexoQual Version: 1.30.0 Depends: R (>= 3.5.0), GenomicAlignments (>= 1.0.1) Imports: methods, utils, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>= 1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>= 1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>= 1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5), scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27), rmarkdown Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat License: GPL (>= 2) MD5sum: 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knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: 879537601116492d40afba2212f7e0f0 NeedsCompilation: no File: CircSeqAlignTk_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: CircStats Version: 0.2-6 Depends: MASS, boot License: GPL-2 MD5sum: cdc066f1a7dc3afd42793aafd90888c4 NeedsCompilation: no File: CircStats_0.2-6_R_x86_64-pc-linux-gnu.tar.gz Package: CiteFuse Version: 1.18.0 Depends: R (>= 4.0) Imports: SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>= 1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid, dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales, scran (>= 1.14.6), graphics, methods, stats, utils, reshape2, ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5, rlang, Rcpp, compositions LinkingTo: Rcpp Suggests: knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle, pkgdown License: GPL-3 MD5sum: 48e32b5ca7e20425c51072104f822aaa NeedsCompilation: yes File: CiteFuse_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: Ckmeans.1d.dp Version: 4.3.5 Imports: Rcpp, Rdpack (>= 0.6-1) LinkingTo: Rcpp Suggests: testthat, knitr, rmarkdown, RColorBrewer License: LGPL (>= 3) MD5sum: e726a2a0598ee12ac4116a7de8c0b0ae NeedsCompilation: yes File: Ckmeans.1d.dp_4.3.5_R_x86_64-pc-linux-gnu.tar.gz Package: ClassifyR Version: 3.10.6 Depends: R (>= 4.1.0), generics, methods, S4Vectors, MultiAssayExperiment, BiocParallel, survival Imports: grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2 (>= 3.0.0), ggpubr, reshape2, ggupset, broom, dcanr Suggests: limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet, class, randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale License: GPL-3 MD5sum: a47423728cda465f3cd559aa7e596495 NeedsCompilation: yes File: ClassifyR_3.10.6_R_x86_64-pc-linux-gnu.tar.gz Package: CleanUpRNAseq Version: 1.0.0 Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, GenomeInfoDb, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5e28040debd787d913ec7025d3f30f54 NeedsCompilation: no File: CleanUpRNAseq_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: Clomial Version: 1.42.0 Depends: R (>= 2.10), matrixStats Imports: methods, permute License: GPL (>= 2) MD5sum: 883e4dd3881386ad2f92dae390414a03 NeedsCompilation: no File: Clomial_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: CluMSID Version: 1.22.0 Depends: R (>= 3.6) Imports: mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally, ggplot2, plotly, methods, utils, stats, sna, grDevices, graphics, Biobase, gplots, MSnbase Suggests: knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr, CluMSIDdata, metaMS, metaMSdata, xcms License: MIT + file LICENSE MD5sum: 9a6b0efaf108322e3b698a2d221384c6 NeedsCompilation: no File: CluMSID_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: CluMSIDdata Version: 1.22.0 Depends: R (>= 3.6) License: MIT + file LICENSE MD5sum: 27ad553e1d8bc097d542831f6c05ff0e NeedsCompilation: no File: CluMSIDdata_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: ClueR Version: 1.4.2 Depends: R (>= 2.10.0) Imports: e1071, parallel, stats, graphics, grDevices License: GPL-3 MD5sum: 11ecaaae76485f0a333c866a97db494d NeedsCompilation: no File: ClueR_1.4.2_R_x86_64-pc-linux-gnu.tar.gz Package: ClustAll Version: 1.2.0 Depends: R (>= 4.2.0) Imports: FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach, dplyr, fpc, mice, modeest, flock, networkD3, methods, ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices, ggplot2, grid, stats, utils, pbapply Suggests: RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, 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kableExtra, scRNAseq, BiocStyle License: Artistic-2.0 MD5sum: 4894589ab50df1dfd915fce4d9af3068 NeedsCompilation: no File: ClusterFoldSimilarity_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: ClusterJudge Version: 1.28.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 308ee1dce2918474ca0c2d84ddf2243f NeedsCompilation: no File: ClusterJudge_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: ClusterR Version: 1.3.3 Depends: R(>= 3.2) Imports: Rcpp (>= 0.12.5), graphics, grDevices, utils, stats, gmp, ggplot2, lifecycle LinkingTo: Rcpp, RcppArmadillo (>= 0.9.1) Suggests: OpenImageR, FD, testthat, covr, knitr, rmarkdown License: GPL-3 MD5sum: 1385a13069236daeb4558dc40fc1a667 NeedsCompilation: yes File: ClusterR_1.3.3_R_x86_64-pc-linux-gnu.tar.gz Package: ClusterSignificance Version: 1.34.0 Depends: R (>= 3.3.0) Imports: methods, pracma, princurve (>= 2.0.5), 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knitr, rmarkdown, covr, tibble, ggplot2movies, vdiffr, jsonlite, data.table License: MIT + file LICENSE MD5sum: 85574fe0f5d832dccfd95e35386cea30 NeedsCompilation: no File: ComplexUpset_1.3.3_R_x86_64-pc-linux-gnu.tar.gz Package: CompoundDb Version: 1.10.0 Depends: R (>= 4.1), methods, AnnotationFilter, S4Vectors Imports: BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr, RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: 9cca579d40c9872c960ffdc7c65a5798 NeedsCompilation: no File: CompoundDb_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: ConsRank Version: 2.1.4 Depends: rgl Imports: rlist (>= 0.4.2), methods, proxy, gtools, tidyr License: GPL-3 MD5sum: 116040b0bf9d79c91ad6e986aa5545b7 NeedsCompilation: no File: ConsRank_2.1.4_R_x86_64-pc-linux-gnu.tar.gz Package: ConsensusClusterPlus Version: 1.70.0 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Package: DNABarcodes Version: 1.36.0 Depends: Matrix, parallel Imports: Rcpp (>= 0.11.2), BH LinkingTo: Rcpp, BH Suggests: knitr, BiocStyle, rmarkdown License: GPL-2 MD5sum: 5024ac4a3d91b7189027e81cd8483516 NeedsCompilation: yes File: DNABarcodes_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: DNAcopy Version: 1.80.0 License: GPL (>= 2) MD5sum: 08d7b5af5071538590547cb42e11d53f NeedsCompilation: yes File: DNAcopy_1.80.0_R_x86_64-pc-linux-gnu.tar.gz Package: DNAfusion Version: 1.8.0 Depends: R (>= 4.2.0) Imports: bamsignals, GenomicRanges, IRanges, Rsamtools, GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics Suggests: knitr, rmarkdown, testthat, sessioninfo, BiocStyle License: GPL-3 MD5sum: 45fd1ef14edb15a8145f299669dcf451 NeedsCompilation: no File: DNAfusion_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: DNAshapeR Version: 1.34.0 Depends: R (>= 3.4), GenomicRanges Imports: Rcpp (>= 0.12.1), Biostrings, fields LinkingTo: Rcpp Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret License: GPL-2 MD5sum: 7a9c4392c04a24b3a8d753fe48c1c44c NeedsCompilation: yes File: DNAshapeR_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: DO.db Version: 2.9 Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7) Imports: methods, AnnotationDbi License: Artistic-2.0 MD5sum: 8ff0187a57265029011c4694839b2952 NeedsCompilation: no File: DO.db_2.9_R_x86_64-pc-linux-gnu.tar.gz Package: DOSE Version: 4.0.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>= 2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils (>= 0.1.6) Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat License: Artistic-2.0 MD5sum: 8c6e18cb37fb305f6bfc6c98c1c1434f NeedsCompilation: no File: DOSE_4.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: DRIMSeq Version: 1.34.0 Depends: R (>= 3.4.0) Imports: utils, stats, MASS, GenomicRanges, IRanges, S4Vectors, BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2, reshape2 Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat License: GPL (>= 3) MD5sum: b5b2915c3a544a645dfc9931b232b921 NeedsCompilation: no File: DRIMSeq_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: DSS Version: 2.54.0 Depends: R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel Imports: utils, graphics, stats, splines Suggests: BiocStyle, knitr, rmarkdown, edgeR License: GPL MD5sum: e72407a1a4b39438228d316985955fa8 NeedsCompilation: yes File: DSS_2.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: DTA Version: 2.52.0 Depends: R (>= 2.10), LSD Imports: scatterplot3d License: Artistic-2.0 MD5sum: d7a010f8978be721a0237d89484a290d NeedsCompilation: no File: DTA_2.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: DT Version: 0.33 Imports: htmltools (>= 0.3.6), htmlwidgets (>= 1.3), httpuv, jsonlite (>= 0.9.16), magrittr, crosstalk, jquerylib, promises Suggests: knitr (>= 1.8), rmarkdown, shiny (>= 1.6), bslib, future, testit, tibble License: GPL-3 | file LICENSE MD5sum: 63a4bc46009e676d036a0a255f3c4e89 NeedsCompilation: no File: DT_0.33_R_x86_64-pc-linux-gnu.tar.gz Package: DaMiRseq Version: 2.18.0 Depends: R (>= 3.5.0), SummarizedExperiment, ggplot2 Imports: DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap, FactoMineR, corrplot, randomForest, e1071, caret, MASS, lubridate, plsVarSel, kknn, FSelector, methods, stats, utils, graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR, plyr Suggests: BiocStyle, knitr, testthat License: GPL (>= 2) MD5sum: 89f3a39dacd31f013ccd9b22fae14e81 NeedsCompilation: no File: DaMiRseq_2.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: Damsel Version: 1.2.0 Depends: R (>= 4.4.0) Imports: AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2, goseq, magrittr, patchwork, plyranges, reshape2, rlang, Rsamtools, Rsubread, stats, stringr, tidyr, utils Suggests: BiocStyle, biomaRt, biovizBase, BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db, rmarkdown, testthat (>= 3.0.0), TxDb.Dmelanogaster.UCSC.dm6.ensGene License: MIT + file LICENSE MD5sum: 9729ea4e6d54446b809487b14f06f70e NeedsCompilation: no File: Damsel_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: DataVisualizations Version: 1.3.3 Depends: R (>= 3.5) Imports: Rcpp (>= 0.12.12), ggplot2, sp, pracma, reshape2 LinkingTo: Rcpp, RcppArmadillo Suggests: plyr, MBA, ggmap, plotrix, rworldmap, rgl, ABCanalysis, choroplethr, R6, parallelDist, knitr (>= 1.12), rmarkdown (>= 0.9), vioplot, ggExtra, plotly, htmlwidgets, diptest, moments, signal, ggrepel, MASS, ROCit, ScatterDensity (>= 0.0.3), colorspace, viridis, gridExtra License: GPL-3 MD5sum: 7b04f689c770f35198a2c97057c4a5d7 NeedsCompilation: yes File: DataVisualizations_1.3.3_R_x86_64-pc-linux-gnu.tar.gz Package: DeMAND Version: 1.36.0 Depends: R (>= 2.14.0), KernSmooth, methods License: file LICENSE 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BiocGenerics (>= 0.13.8), Biobase (>= 2.17.8), annotate (>= 1.45.3), methods, graph (>= 1.37.2) Imports: AnnotationDbi, XML Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr, RUnit License: Artistic-2.0 MD5sum: 1c9ffc4a666481e590fa8798fc409cbd NeedsCompilation: no File: GSEABase_1.68.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSEABenchmarkeR Version: 1.26.0 Depends: R (>= 3.5.0), Biobase, SummarizedExperiment Imports: AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel, edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods, S4Vectors, stats, utils Suggests: BiocStyle, GSE62944, knitr, rappdirs, rmarkdown License: Artistic-2.0 MD5sum: c3de23c63244cbd8bd4ce891290df251 NeedsCompilation: no File: GSEABenchmarkeR_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSEAlm Version: 1.66.0 Depends: Biobase Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer License: Artistic-2.0 MD5sum: 796b5cb4cdd59bfacbff171c847e59c1 NeedsCompilation: no File: GSEAlm_1.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSEAmining Version: 1.16.0 Depends: R (>= 4.0) Imports: dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud, stringr, gridExtra, rlang, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm License: GPL-3 | file LICENSE MD5sum: 6fa964bcd07fe5f02885a7ab36a89e83 NeedsCompilation: no File: GSEAmining_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSRI Version: 2.54.0 Depends: R (>= 2.14.2), fdrtool Imports: methods, graphics, stats, utils, genefilter, Biobase, GSEABase, les (>= 1.1.6) Suggests: limma, hgu95av2.db Enhances: parallel License: GPL-3 MD5sum: c4fa4d94a343ced2ad3a36ee8da7c387 NeedsCompilation: no File: GSRI_2.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSReg Version: 1.40.0 Depends: R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures, AnnotationDbi Suggests: GenomicRanges, GSBenchMark License: GPL-2 MD5sum: 0b0bc64b09b9edd37d29bbd611499371 NeedsCompilation: yes File: GSReg_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSVA Version: 2.0.5 Depends: R (>= 3.5.0) Imports: methods, stats, utils, graphics, S4Vectors, IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel, BiocParallel, SingleCellExperiment, SpatialExperiment, sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array, BiocSingular, cli LinkingTo: cli Suggests: BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny, shinydashboard, ggplot2, data.table, plotly, future, promises, shinybusy, shinyjs License: GPL (>= 2) MD5sum: 8d3cacbb564f04d94095b5bb39f939be NeedsCompilation: yes File: GSVA_2.0.5_R_x86_64-pc-linux-gnu.tar.gz Package: GSVAdata Version: 1.42.0 Depends: R (>= 3.5), Biobase, GSEABase, hgu95a.db, SummarizedExperiment License: Artistic-2.0 MD5sum: cab8effa632323b704a2737b2e029cc9 NeedsCompilation: no File: GSVAdata_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: GSgalgoR Version: 1.16.0 Imports: cluster, doParallel, foreach, matchingR, nsga2R, survival, proxy, stats, methods, Suggests: knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp, Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP, iC10TrainingData, pamr, testthat License: MIT + file LICENSE MD5sum: 2a8c9dd038f32d81e126f9e7e4b688fe NeedsCompilation: no File: GSgalgoR_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: GUIDEseq Version: 1.36.0 Depends: R (>= 3.5.0), GenomicRanges, BiocGenerics Imports: Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table, matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors (>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3), GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures, rio, tidyr, tools, methods, purrr, ggplot2, openxlsx, patchwork, rlang Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: ce58e81d2579409033ab5400119ef0e8 NeedsCompilation: no File: GUIDEseq_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: GUniFrac Version: 1.8 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.13), vegan, ggplot2, matrixStats, Matrix, ape, parallel, stats, utils, statmod, rmutil, dirmult, MASS, ggrepel, foreach, modeest, inline, methods LinkingTo: Rcpp Suggests: ade4, knitr, markdown, ggpubr License: GPL-3 MD5sum: 4ec508c63cdeeaf634a3683c6f34cd09 NeedsCompilation: yes File: GUniFrac_1.8_R_x86_64-pc-linux-gnu.tar.gz Package: GWAS.BAYES Version: 1.16.0 Depends: R (>= 4.3.0) Imports: GA (>= 3.2), caret (>= 6.0-86), memoise (>= 1.1.0), Matrix (>= 1.2-18), limma (>= 3.54.0), stats (>= 4.2.2), MASS (>= 7.3-58.1) Suggests: BiocStyle, knitr, rmarkdown, formatR, rrBLUP License: GPL-3 + file LICENSE MD5sum: 2a092f6f06e2390a1e966561721fa81a NeedsCompilation: no File: GWAS.BAYES_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: GWASExactHW Version: 1.2 License: GPL-3 MD5sum: 934d9dd3829bc0acb5d53250d5fad56f NeedsCompilation: yes File: GWASExactHW_1.2_R_x86_64-pc-linux-gnu.tar.gz Package: GWASTools Version: 1.52.0 Depends: Biobase Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, data.table Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel, BiocStyle, knitr License: Artistic-2.0 MD5sum: 7016dbd9fe9302f8d0484fa5ac368631 NeedsCompilation: no File: GWASTools_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: GWASdata Version: 1.44.0 Depends: GWASTools Suggests: ncdf4 License: Artistic-2.0 MD5sum: aa2ce260293926b4f697e9eaefbd4a5f NeedsCompilation: no File: GWASdata_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: GWENA Version: 1.16.0 Depends: R (>= 4.1) Imports: WGCNA (>= 1.67), dplyr (>= 0.8.3), dynamicTreeCut (>= 1.63-1), ggplot2 (>= 3.1.1), gprofiler2 (>= 0.1.6), magrittr (>= 1.5), tibble (>= 2.1.1), tidyr (>= 1.0.0), NetRep (>= 1.2.1), igraph (>= 1.2.4.1), RColorBrewer (>= 1.1-2), purrr (>= 0.3.3), rlist (>= 0.4.6.1), matrixStats (>= 0.55.0), SummarizedExperiment (>= 1.14.1), stringr (>= 1.4.0), cluster (>= 2.1.0), grDevices (>= 4.0.4), methods, graphics, stats, utils Suggests: testthat (>= 2.1.0), knitr (>= 1.25), rmarkdown (>= 1.16), prettydoc (>= 0.3.0), httr (>= 1.4.1), S4Vectors (>= 0.22.1), BiocStyle (>= 2.15.8) License: GPL-3 MD5sum: 1ba26e25484317c63cd5675ba7f14e2b NeedsCompilation: no File: GWENA_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: GateFinder Version: 1.26.0 Imports: splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 1680d379d1a5f87e281380a5dc5f633f NeedsCompilation: no File: GateFinder_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeDi Version: 1.2.0 Depends: R (>= 4.4.0) Imports: GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders, fontawesome, grDevices, parallel, stats, ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools, BiocParallel, BiocFileCache, cluster, circlize Suggests: knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools, pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 4ccdfe1bde8ff88e7b24804abd25eaaf NeedsCompilation: no File: GeDi_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenProSeq Version: 1.10.0 Depends: keras, mclust, R (>= 4.2) Imports: tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders, reticulate, stats Suggests: VAExprs, stringdist, knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: 8e0e66489716598b7a36baccf1514571 NeedsCompilation: no File: GenProSeq_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenSA Version: 1.1.14.1 Depends: R (>= 2.12.0) License: GPL-2 MD5sum: 2de5a567e3d91721b4717504a4eabff7 NeedsCompilation: yes File: GenSA_1.1.14.1_R_x86_64-pc-linux-gnu.tar.gz Package: GenVisR Version: 1.38.0 Depends: R (>= 3.3.0), methods Imports: AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings, DBI, GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr (>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table, BSgenome, GenomeInfoDb, VariantAnnotation Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 License: GPL-3 + file LICENSE MD5sum: 6297d518f6767bca9df0b15f91b6ba1a NeedsCompilation: no File: GenVisR_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneBreak Version: 1.36.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 4db27c1c8e8ce65db25d6cb75db9241d NeedsCompilation: no File: GeneBreak_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneExpressionSignature Version: 1.52.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: baa1ab53a94f71b072100c3bb8a55f81 NeedsCompilation: no File: GeneExpressionSignature_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneGA Version: 1.56.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: cf8c0245717d04c07bfb7434247173a6 NeedsCompilation: no File: GeneGA_1.56.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneMeta Version: 1.78.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: c83a526a7673bf0ac4725ce9837deb67 NeedsCompilation: no File: GeneMeta_1.78.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneNet Version: 1.2.16 Depends: R (>= 3.0.2), corpcor (>= 1.6.10), longitudinal (>= 1.1.13), fdrtool (>= 1.2.17) Imports: stats, grDevices Suggests: graph, Rgraphviz License: GPL (>= 3) MD5sum: d20541b85cd23cb2ff610661c8ba5308 NeedsCompilation: no File: GeneNet_1.2.16_R_x86_64-pc-linux-gnu.tar.gz Package: GeneNetworkBuilder Version: 1.48.0 Depends: R (>= 2.15.1), Rcpp (>= 0.9.13) Imports: plyr, graph, htmlwidgets, Rgraphviz, RCy3, rjson, XML, methods, grDevices, stats, graphics LinkingTo: Rcpp Suggests: RUnit, BiocGenerics, RBGL, knitr, shiny, STRINGdb, BiocStyle, magick, rmarkdown, org.Hs.eg.db License: GPL (>= 2) MD5sum: 7fb79ce85286369fa951ff9b1b7c88a1 NeedsCompilation: yes File: GeneNetworkBuilder_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneOverlap Version: 1.42.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 8d12f80f413c8e7b7f4cc0a6a88777d1 NeedsCompilation: no File: GeneOverlap_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneSelectMMD Version: 2.50.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: e032fb2d1969cad9769b26bccffef4ac NeedsCompilation: yes File: GeneSelectMMD_2.50.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneStructureTools Version: 1.26.0 Imports: Biostrings,GenomicRanges,IRanges,data.table,plyr,stringdist,stringr,S4Vectors,BSgenome.Mmusculus.UCSC.mm10,stats,utils,Gviz,rtracklayer,methods Suggests: BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: d2f399ca401bed77f99772e103526212 NeedsCompilation: no File: GeneStructureTools_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: GeneTonic Version: 3.0.0 Depends: R (>= 4.0.0) Imports: AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize, colorspace, colourpicker, ComplexHeatmap, ComplexUpset, dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce, ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics, grDevices, grid, igraph, matrixStats, methods, mosdef (>= 1.1.0), plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors, scales, shiny, shinyAce, shinycssloaders, shinyWidgets, stats, SummarizedExperiment, tidyr, tippy, tools, utils, viridis, visNetwork Suggests: knitr, BiocStyle, htmltools, clusterProfiler, macrophage, org.Hs.eg.db, magrittr, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 22a959c52ef3b7db679814b8c509d249 NeedsCompilation: no File: GeneTonic_3.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomAutomorphism Version: 1.8.1 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, GenomeInfoDb, GenomicRanges, IRanges, matrixStats, XVector, dplyr, data.table, parallel, doParallel, foreach, methods, S4Vectors, stats, numbers, utils Suggests: spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr License: Artistic-2.0 MD5sum: 5d109c729983254d7c7da5ae16d7d734 NeedsCompilation: no File: GenomAutomorphism_1.8.1_R_x86_64-pc-linux-gnu.tar.gz Package: GenomeInfoDbData Version: 1.2.13 Depends: R (>= 3.5.0) License: Artistic-2.0 MD5sum: 2e39d2aea9b1c1e2dff10786768d3382 NeedsCompilation: no File: GenomeInfoDbData_1.2.13_R_x86_64-pc-linux-gnu.tar.gz Package: GenomeInfoDb Version: 1.42.3 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.25.12), IRanges (>= 2.13.12) Imports: stats, stats4, utils, UCSC.utils, GenomeInfoDbData Suggests: R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr License: Artistic-2.0 MD5sum: bd02318eed3247adb20fe5d6695601ef NeedsCompilation: no File: GenomeInfoDb_1.42.3_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicAlignments Version: 1.42.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), GenomicRanges (>= 1.55.3), SummarizedExperiment (>= 1.9.13), Biostrings (>= 2.55.7), Rsamtools (>= 1.31.2) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel LinkingTo: S4Vectors, IRanges Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, knitr, BiocStyle License: Artistic-2.0 MD5sum: 1676937d38e5181c3a092de71334707e NeedsCompilation: yes File: GenomicAlignments_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicDataCommons Version: 1.30.1 Depends: R (>= 4.1.0) Imports: stats, httr, xml2, jsonlite, utils, rlang, readr, GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools, BiocParallel, TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools, R.utils, data.table License: Artistic-2.0 MD5sum: bcd093225445e9afdeb33f068b3a09a0 NeedsCompilation: no File: GenomicDataCommons_1.30.1_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicDistributionsData Version: 1.14.0 Depends: R (>= 4.1) Imports: ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter, data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, ensembldb Suggests: knitr, BiocStyle, rmarkdown License: BSD_2_clause + file LICENSE MD5sum: adb95fffa85481b528085946ac514eeb NeedsCompilation: no File: GenomicDistributionsData_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicDistributions Version: 1.14.0 Depends: R (>= 4.0), IRanges, GenomicRanges Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures License: BSD_2_clause + file LICENSE MD5sum: c0be6b0a22742347162d8dcee9e1da01 NeedsCompilation: no File: GenomicDistributions_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicFeatures Version: 1.58.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.17.29), IRanges (>= 2.37.1), GenomeInfoDb (>= 1.35.8), GenomicRanges (>= 1.55.2), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings, rtracklayer Suggests: txdbmaker, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Celegans.UCSC.ce11.ensGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene (>= 3.4.7), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6), SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), 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S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: 503f2ec929640905ec6bec5e29d556b2 NeedsCompilation: no File: GenomicInteractionNodes_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicInteractions Version: 1.40.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr, Gviz, Biobase, graphics, stats, utils, grDevices Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL-3 MD5sum: 0d146c9ae03541fda1af61b1a692a2f7 NeedsCompilation: no File: GenomicInteractions_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: GenomicOZone Version: 1.20.0 Depends: R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt, ggplot2 Imports: grDevices, stats, utils, plyr, gridExtra, lsr, parallel, ggbio, S4Vectors, 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GPL-3 + file LICENCE MD5sum: f2bea0683b04590048a3670ef9cd153a NeedsCompilation: yes File: Harman_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: HarmonizR Version: 1.4.0 Depends: R (>= 4.2.0) Imports: doParallel (>= 1.0.16), foreach (>= 1.5.1), janitor (>= 2.1.0), plyr (>= 1.8.6), sva (>= 3.36.0), seriation (>= 1.3.5), limma (>= 3.46.0), SummarizedExperiment Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 29362a99bdc557d6dd4883ed67131d00 NeedsCompilation: no File: HarmonizR_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: Harshlight Version: 1.78.0 Depends: R (>= 2.10) Imports: affy, altcdfenvs, Biobase, stats, utils License: GPL (>= 2) MD5sum: cd5272e88518e061351d9ab895ac1d53 NeedsCompilation: yes File: Harshlight_1.78.0_R_x86_64-pc-linux-gnu.tar.gz Package: Heatplus Version: 3.14.0 Imports: graphics, grDevices, stats, RColorBrewer Suggests: Biobase, hgu95av2.db, limma License: GPL (>= 2) MD5sum: 2032689f6a47f76c26538a87f96cb1cc NeedsCompilation: no File: 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BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix, BiocFileCache, rappdirs Enhances: parallel License: GPL-3 MD5sum: 40616c10a7184700862b7e71c4878fbe NeedsCompilation: yes File: HiCDCPlus_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: HiCDOC Version: 1.8.0 Depends: InteractionSet, GenomicRanges, SummarizedExperiment, R (>= 4.1.0) Imports: methods, zlibbioc, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools, pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra, data.table, multiHiCcompare, GenomeInfoDb LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5 License: LGPL-3 MD5sum: 91798236161f86da571090fbc0424849 NeedsCompilation: yes File: HiCDOC_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: HiCDataHumanIMR90 Version: 1.26.0 Depends: R (>= 3.5.0) Suggests: HiTC, BiocStyle License: GPL-3 MD5sum: 7a9dd11d0c75636c0e9463d325e8a55f NeedsCompilation: no File: HiCDataHumanIMR90_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: HiCDataLymphoblast Version: 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3c20c66ece62cf8bd829365e51df8530 NeedsCompilation: no File: HiCcompare_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: HiContactsData Version: 1.8.0 Depends: ExperimentHub Imports: BiocFileCache, AnnotationHub Suggests: testthat, methods, BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: d544185d4a86d29158faf8757faf49c5 NeedsCompilation: no File: HiContactsData_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: HiContacts Version: 1.8.0 Depends: R (>= 4.2), HiCExperiment Imports: InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 55ee339bdd16f5da8b150d8bd784a27e NeedsCompilation: no File: 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GenomicRanges, Biostrings, graphics, gtools, IRanges, methods, stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer, preprocessCore Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle License: GPL (>= 2) MD5sum: 6d93ceddc692220bcd9c4f735a02d2b4 NeedsCompilation: no File: MEDIPS_1.58.0_R_x86_64-pc-linux-gnu.tar.gz Package: MEDME Version: 1.66.0 Depends: R (>= 2.15), grDevices, graphics, methods, stats, utils Imports: Biostrings, MASS, drc Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 License: GPL (>= 2) MD5sum: d3a2567839e1dd025e6ef78a9402ce00 NeedsCompilation: yes File: MEDME_1.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: MEEBOdata Version: 1.44.0 License: LGPL MD5sum: 9c778e60b676a4fb55f966b677b75eb1 NeedsCompilation: no File: MEEBOdata_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: MEIGOR Version: 1.40.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 MD5sum: 5ea3f538ffff85132248a24e264190b1 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535e6867d0eaab5688b69b6902b2369f NeedsCompilation: yes File: MSstats_4.14.1_R_x86_64-pc-linux-gnu.tar.gz Package: MVCClass Version: 1.80.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 8f30a74b147b262a3655c3a6b52280ed NeedsCompilation: no File: MVCClass_1.80.0_R_x86_64-pc-linux-gnu.tar.gz Package: MWASTools Version: 1.30.0 Depends: R (>= 3.5.0) Imports: glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra, igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST, ComplexHeatmap, stats, utils Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: CC BY-NC-ND 4.0 MD5sum: 522a6fd0e4efd415ff157b269d568e6b NeedsCompilation: no File: MWASTools_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: Maaslin2 Version: 1.20.0 Depends: R (>= 3.6) Imports: robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap, logging, data.table, lmerTest, hash, optparse, grDevices, stats, utils, glmmTMB, MASS, cplm, pscl, lme4, tibble Suggests: 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mygene Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 7a4e5b51275ebe98c8a40f8d78a52c3e NeedsCompilation: no File: MetaboSignal_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: MethPed Version: 1.34.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 5114601e418679160014d871280bdf5a NeedsCompilation: no File: MethPed_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: MethReg Version: 1.16.0 Depends: R (>= 4.0) Imports: dplyr, plyr, GenomicRanges, SummarizedExperiment, DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors, sesameData, sesame, AnnotationHub, ExperimentHub, stringr, readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges, sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite, TFBSTools Suggests: rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils, doParallel, reshape2, motifmatchr, matrixStats, biomaRt, dorothea, viper, stageR, 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grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: 30279d17da095aae94798c7125afeaa3 NeedsCompilation: no File: MoonlightR_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: Motif2Site Version: 1.10.0 Depends: R (>= 4.1) Imports: S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805 License: GPL-2 MD5sum: 38a012edea48d15e0f9341ad6181e169 NeedsCompilation: no File: Motif2Site_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: MotifDb Version: 1.48.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, 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splines, MassSpecWavelet, signal Suggests: knitr, rmarkdown, ggpubr, conflicted License: MIT + file LICENSE MD5sum: 315077516ab02fd9e49481b425704596 NeedsCompilation: no File: NMRphasing_1.0.6_R_x86_64-pc-linux-gnu.tar.gz Package: NOISeq Version: 2.50.0 Depends: R (>= 2.13.0), methods, Biobase (>= 2.13.11), splines (>= 3.0.1), Matrix (>= 1.2) License: Artistic-2.0 MD5sum: 3ef144e6fefd680c22823b7cd4342006 NeedsCompilation: no File: NOISeq_2.50.0_R_x86_64-pc-linux-gnu.tar.gz Package: NPARC Version: 1.18.0 Depends: R (>= 4.0.0) Imports: dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr, stats, methods Suggests: testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2, BiocStyle License: GPL-3 MD5sum: 98dd20c73e54161328f2df3f1f1b84da NeedsCompilation: no File: NPARC_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: NTW Version: 1.56.0 Depends: R (>= 2.3.0) Imports: mvtnorm, stats, utils License: GPL-2 MD5sum: 3a6ba01fea5e91eee0e1761cc4a28999 NeedsCompilation: no File: 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NanoTube_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: NanoporeRNASeq Version: 1.16.0 Depends: R(>= 4.0.0), ExperimentHub (>= 1.15.3) Suggests: knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize, ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments, Rsamtools Enhances: parallel License: GPL-3 + file LICENSE MD5sum: d2f9139108258893ce6d0e3e86d87da5 NeedsCompilation: no File: NanoporeRNASeq_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: NbClust Version: 3.0.1 Depends: R (>= 3.1.0) License: GPL-2 MD5sum: 87becffed0222921f1bcffe3fb6fc745 NeedsCompilation: no File: NbClust_3.0.1_R_x86_64-pc-linux-gnu.tar.gz Package: Nebulosa Version: 1.16.0 Depends: R (>= 4.0), ggplot2, patchwork Imports: SingleCellExperiment, SummarizedExperiment, SeuratObject, ks, Matrix, stats, methods, ggrastr Suggests: testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran, DropletUtils, igraph, BiocFileCache, Seurat License: GPL-3 MD5sum: 6113e03ddd616a6271d555ed0837f01b NeedsCompilation: no File: Nebulosa_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: NetActivityData Version: 1.8.0 Depends: R (>= 4.2.0) Suggests: BiocStyle, knitr License: MIT + file LICENSE MD5sum: 239f12de225411b126c7197fc9b90130 NeedsCompilation: no File: NetActivityData_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: NetActivity Version: 1.8.0 Depends: R (>= 4.1.0) Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse License: MIT + file LICENSE MD5sum: ec52e65ab976e59fa4f72cf2fe78c152 NeedsCompilation: no File: NetActivity_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: NetRep Version: 1.2.7 Depends: R (>= 3.6), methods Imports: foreach, Rcpp (>= 0.11), statmod, RhpcBLASctl, abind, RColorBrewer, utils, stats, graphics, grDevices LinkingTo: Rcpp, BH, RcppArmadillo (>= 0.4) Suggests: bigmemory, testthat, knitr, rmarkdown License: GPL-2 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BiocStyle, knitr License: GPL-3 MD5sum: 3bea7eef94c5057f35769f02062a849b NeedsCompilation: no File: NewWave_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: NoRCE Version: 1.18.0 Depends: R (>= 4.2.0) Imports: KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,GenomeInfoDb, S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl, dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,zlibbioc, biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi Suggests: knitr, TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene, testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown, TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene, org.Mm.eg.db, org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics, org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,markdown License: MIT + file LICENSE MD5sum: 3e90e7f7d953e79ecbcf78ca9f98fb39 NeedsCompilation: no File: NoRCE_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: NormalyzerDE Version: 1.24.0 Depends: R (>= 4.1.0) Imports: vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle License: Artistic-2.0 MD5sum: d413f665895b0bcf42a02b0ad394a0fe NeedsCompilation: no File: NormalyzerDE_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: NormqPCR Version: 1.52.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 13e64371fcaa5ee5772e1f45ad826b30 NeedsCompilation: no File: NormqPCR_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: Nozzle.R1 Version: 1.1-1.1 License: LGPL-2 MD5sum: 777762967cbc7d3c442495a40fc012fe NeedsCompilation: no File: Nozzle.R1_1.1-1.1_R_x86_64-pc-linux-gnu.tar.gz Package: NuPoP Version: 2.14.0 Depends: R (>= 4.0) Imports: graphics, utils Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 2489336b1c1b53358c47099586036981 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knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: 41ab0a70e8bfdd9f2843198b4c0653d8 NeedsCompilation: no File: OMICsPCA_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: OMICsPCAdata Version: 1.24.0 Depends: R (>= 3.5.0), MultiAssayExperiment Suggests: knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: ce1cb4699d7f010103a7946aa277d644 NeedsCompilation: no File: OMICsPCAdata_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: OPWeight Version: 1.28.0 Depends: R (>= 3.4.0), Imports: graphics, qvalue, MASS, tibble, stats, Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat License: Artistic-2.0 MD5sum: 59ee9bd969591bdeecf3c33e98c6a24d NeedsCompilation: no File: OPWeight_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: ORFhunteR Version: 1.14.0 Depends: Biostrings, rtracklayer, Peptides Imports: Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table, stringr, randomForest, xfun, stats, utils, parallel, graphics LinkingTo: Rcpp Suggests: knitr, BiocStyle, rmarkdown License: MIT License MD5sum: 4346dfd645b4a14fc38645d9f5520d03 NeedsCompilation: yes File: ORFhunteR_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: ORFik Version: 1.26.2 Depends: R (>= 4.1.0), IRanges (>= 2.17.1), GenomicRanges (>= 1.35.1), GenomicAlignments (>= 1.19.0) Imports: AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt, biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1), BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0), data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2), GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite, methods (>= 3.6.0), R.utils, Rcpp (>= 1.0.0), Rsamtools (>= 1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment (>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils, XML, xml2 (>= 1.2.0), withr LinkingTo: Rcpp Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19 License: MIT + file LICENSE MD5sum: 1a57d3e4955aba4baf25ddf01fa092a2 NeedsCompilation: yes File: ORFik_1.26.2_R_x86_64-pc-linux-gnu.tar.gz Package: OSAT Version: 1.54.0 Depends: methods,stats Suggests: xtable, Biobase License: Artistic-2.0 MD5sum: 176da09e91d5349a9fcf98959f13db87 NeedsCompilation: no File: OSAT_1.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: OTUbase Version: 1.56.0 Depends: R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>= 1.23.15), Biobase, vegan Imports: Biostrings License: Artistic-2.0 MD5sum: 5d8ac546c1dc1d5c19bb31b4f2d2f996 NeedsCompilation: no File: OTUbase_1.56.0_R_x86_64-pc-linux-gnu.tar.gz Package: OUTRIDER Version: 1.24.0 Depends: R (>= 3.6), BiocParallel, GenomicFeatures, SummarizedExperiment, data.table, methods Imports: BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics, GenomicRanges, ggplot2, ggrepel, grDevices, heatmaply, pheatmap, graphics, IRanges, matrixStats, plotly, plyr, pcaMethods, PRROC, RColorBrewer, reshape2, S4Vectors, scales, splines, stats, txdbmaker, utils LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB, AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase License: MIT + file LICENSE MD5sum: 5ca061069c13e27f823a091a46682afb NeedsCompilation: yes File: OUTRIDER_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: OVESEG Version: 1.22.0 Depends: R (>= 3.6) Imports: stats, utils, methods, BiocParallel, SummarizedExperiment, limma, fdrtool, Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra, grid, reshape2, scales License: GPL-2 MD5sum: 9f5444008d3459a7262660ecbd65c3ec NeedsCompilation: yes File: OVESEG_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: OlinkAnalyze Version: 4.2.0 Depends: R (>= 4.1.0) Imports: broom, car, cli (>= 3.6.2), dplyr (>= 1.1.1), data.table, emmeans, forcats, generics, ggplot2, ggpubr, ggrepel, grDevices, grid, magrittr, methods, readxl, rlang, rstatix, stats, stringr, tibble, tidyr, tidyselect, tools, utils Suggests: arrow, clusterProfiler, extrafont, FSA, ggplotify, kableExtra, knitr, lme4, lmerTest, markdown, msigdbr, openssl, ordinal, pheatmap, rmarkdown, scales, systemfonts, testthat (>= 3.0.0), umap, vdiffr, withr, zip License: AGPL (>= 3) MD5sum: 0b7b9e5f3e1f79dc75202895f83cb945 NeedsCompilation: no File: OlinkAnalyze_4.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: OmaDB Version: 2.22.0 Depends: R (>= 3.5), httr (>= 1.2.1), plyr(>= 1.8.4) Imports: utils, ape, Biostrings, GenomicRanges, IRanges, methods, topGO, jsonlite Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 8fe113d6e96659d19ce93c8a7c3932df NeedsCompilation: no File: OmaDB_2.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: OmicCircos Version: 1.44.0 Depends: R (>= 2.14.0), methods,GenomicRanges License: GPL-2 MD5sum: 870005c79ff01e0ab37252e40c510afe NeedsCompilation: no File: OmicCircos_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: OmicsMLRepoR Version: 1.0.0 Depends: R (>= 4.4.0) Imports: dplyr, stringr, rols, tidyr, methods, stats, tibble, data.tree, jsonlite, plyr, BiocFileCache, readr, DiagrammeR, rlang, lubridate Suggests: arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>= 3.0.0), cBioPortalData License: Artistic-2.0 MD5sum: 1ea6e17654643c0dd7e184b4396ccb25 NeedsCompilation: no File: OmicsMLRepoR_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: Omixer Version: 1.16.0 Depends: R (>= 4.0.0) Imports: dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr, tidyselect, grid, stats, stringr Suggests: knitr, rmarkdown, BiocStyle, magick, testthat License: MIT + file LICENSE MD5sum: 720ba8adadc25a5f2d5b3d05a86b5cba NeedsCompilation: no File: Omixer_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: OmnipathR Version: 3.14.0 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, testthat License: MIT + file LICENSE MD5sum: ca44f69217f3f5ea1a76f39a88c4bc82 NeedsCompilation: no File: OmnipathR_3.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: OncoScore Version: 1.34.0 Depends: R (>= 4.1.0), Imports: biomaRt, grDevices, graphics, utils, methods, Suggests: BiocGenerics, BiocStyle, knitr, testthat, License: file LICENSE MD5sum: 98c2a1d7ba7de8602813f34f2ae747f7 NeedsCompilation: no File: OncoScore_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: OncoSimulR Version: 4.8.0 Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, stringr LinkingTo: Rcpp Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander License: GPL (>= 3) MD5sum: 4dee886ca43e1e754f1be2b1ca633fe3 NeedsCompilation: yes File: OncoSimulR_4.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: Oncotree Version: 0.3.5 Depends: R (>= 2.3.1), boot Suggests: lattice License: GPL (>= 2) MD5sum: 51ca82832d012aace1cd33e741fb8ee6 NeedsCompilation: no File: Oncotree_0.3.5_R_x86_64-pc-linux-gnu.tar.gz Package: OpenStats Version: 1.18.0 Depends: nlme Imports: MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist, summarytools, graphics, stats, utils Suggests: rmarkdown License: GPL (>= 2) MD5sum: 7c4d1c03e552bb79d76999577fa7c16b NeedsCompilation: no File: OpenStats_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: OrderedList Version: 1.78.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: 62bc7d36e5fbb20561afbdd0f519f07e NeedsCompilation: no File: OrderedList_1.78.0_R_x86_64-pc-linux-gnu.tar.gz Package: OrgMassSpecR Version: 0.5-3 Depends: R (>= 3.0.0), grid Suggests: lattice, knitr, rmarkdown License: BSD_2_clause + file LICENSE MD5sum: 30b0db33828c200a13c7a733fb72dc79 NeedsCompilation: no File: OrgMassSpecR_0.5-3_R_x86_64-pc-linux-gnu.tar.gz Package: Organism.dplyr Version: 1.34.0 Depends: R (>= 3.4), dplyr (>= 0.7.0), AnnotationFilter (>= 1.1.3) Imports: RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges, GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, magick, BiocStyle, ggplot2 License: Artistic-2.0 MD5sum: 34912aec181182842da7d0db52167fc6 NeedsCompilation: no File: Organism.dplyr_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: OrganismDbi Version: 1.48.0 Depends: R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4) Imports: methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL, S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr License: Artistic-2.0 MD5sum: 5c2a64e3124d3e2c47a69b1cf35d53d7 NeedsCompilation: no File: OrganismDbi_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: OutSplice Version: 1.6.0 Depends: R(>= 4.3) Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0), GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0) Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-2 MD5sum: 416fd668ab4ec41f6c1b3e0b62fde638 NeedsCompilation: no File: OutSplice_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: PAA Version: 1.40.0 Depends: R (>= 3.2.0), Rcpp (>= 0.11.6) Imports: e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR, sva LinkingTo: Rcpp Suggests: BiocStyle, RUnit, BiocGenerics, vsn License: BSD_3_clause + file LICENSE MD5sum: 1cfd847f91c3581b20366592dfcd3337 NeedsCompilation: yes File: PAA_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: PADOG Version: 1.48.0 Depends: R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase Imports: limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db, hgu133a.db, KEGGREST, nlme Suggests: doParallel, parallel License: GPL (>= 2) MD5sum: e000012029218bd0bbcfca8d26bb90ca NeedsCompilation: no File: PADOG_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: PAIRADISE Version: 1.22.0 Depends: R (>= 3.6), nloptr Imports: SummarizedExperiment, S4Vectors, stats, methods, abind, BiocParallel Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 44c5c70afed94a561457c6c5055fc68e NeedsCompilation: no File: PAIRADISE_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: PANR Version: 1.52.0 Depends: R (>= 2.14), igraph Imports: graphics, grDevices, MASS, methods, pvclust, stats, utils, RedeR Suggests: snow License: Artistic-2.0 MD5sum: 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LinkingTo: Rcpp Suggests: pander, rmarkdown, knitr, knitcitations, crayon, testthat, markdown, BiocStyle, R.utils License: GPL (>= 3) MD5sum: cbb2ab3be3fc3c760f6e6fbf0a2aa805 NeedsCompilation: yes File: PharmacoGx_3.10.1_R_x86_64-pc-linux-gnu.tar.gz Package: PhenStat Version: 2.42.0 Depends: R (>= 3.5.0) Imports: SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf, knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4, graphics, grDevices, utils, stats Suggests: RUnit, BiocGenerics License: file LICENSE MD5sum: 366086a5513784386dd769835ce36ee2 NeedsCompilation: no File: PhenStat_2.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: PhenoGeneRanker Version: 1.14.0 Imports: igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel Suggests: knitr, rmarkdown License: Creative Commons Attribution 4.0 International License MD5sum: c105ed2b87cdc17a967725aadc452da5 NeedsCompilation: no File: PhenoGeneRanker_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: PhosR Version: 1.16.0 Depends: R (>= 4.2.0) Imports: ruv, e1071, dendextend, limma, pcaMethods, stats, RColorBrewer, circlize, dplyr, igraph, pheatmap, preprocessCore, tidyr, rlang, graphics, grDevices, utils, SummarizedExperiment, methods, S4Vectors, BiocGenerics, ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext, stringi Suggests: testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown, org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle, stringr, calibrate License: GPL-3 + file LICENSE MD5sum: 32fd7135fa76d42cd7fd0a24679bbeed NeedsCompilation: no File: PhosR_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: PhyloProfile Version: 1.20.4 Depends: R (>= 4.4.0) Imports: ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table, dplyr, DT, energy, ExperimentHub, extrafont, fastcluster, ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl, scattermore, shiny, shinyBS, shinycssloaders, shinyFiles, shinyjs, stringr, tsne, umap, xml2, zoo, yaml Suggests: knitr, rmarkdown, testthat, OmaDB License: MIT + file LICENSE MD5sum: b8761a6a86eeff0eae42171d1f676903 NeedsCompilation: no File: PhyloProfile_1.20.4_R_x86_64-pc-linux-gnu.tar.gz Package: Pigengene Version: 1.32.0 Depends: R (>= 4.0.3), graph, BiocStyle (>= 2.28.0) Imports: bnlearn (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit, Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices, graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr, gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI, DOSE Suggests: org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>= 2.30.0), knitr, AnnotationDbi, energy License: GPL (>= 2) MD5sum: e7d45af93f9d7257d5f247cddf39ed18 NeedsCompilation: no File: Pigengene_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: Pirat Version: 1.0.2 Depends: R (>= 4.4.0), BiocManager (>= 1.3.20) Imports: basilisk (>= 1.18.0), reticulate, progress, ggplot2, MASS, invgamma, grDevices, stats, graphics, SummarizedExperiment, S4Vectors Suggests: knitr, BiocStyle License: GPL-2 MD5sum: 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MD5sum: f496c94842b842e2407d4dceeeccddb4 NeedsCompilation: no File: Polychrome_1.5.1_R_x86_64-pc-linux-gnu.tar.gz Package: PolynomF Version: 2.0-8 Depends: R (>= 3.0.0), graphics, grDevices Imports: stats, Rcpp, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 2bb108f9834a287feef7a5f1a78793a3 NeedsCompilation: yes File: PolynomF_2.0-8_R_x86_64-pc-linux-gnu.tar.gz Package: PrInCE Version: 1.22.0 Depends: R (>= 3.6.0) Imports: purrr (>= 0.2.4), dplyr (>= 0.7.4), tidyr (>= 0.8.99), forecast (>= 8.2), progress (>= 1.1.2), Hmisc (>= 4.0), naivebayes (>= 0.9.1), robustbase (>= 0.92-7), ranger (>= 0.8.0), LiblineaR (>= 2.10-8), speedglm (>= 0.3-2), tester (>= 0.1.7), magrittr (>= 1.5), Biobase (>= 2.40.0), MSnbase (>= 2.8.3), stats, utils, methods, Rdpack (>= 0.7) Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: b1baaf270312d21f4458fd587707f4f3 NeedsCompilation: no File: PrInCE_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: Prostar Version: 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BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr License: Artistic-2.0 | file LICENSE MD5sum: b07468557bed48370e2f75716bc4fc3a NeedsCompilation: yes File: Rsamtools_2.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: Rsolnp Version: 1.16 Depends: R (>= 2.10.0) Imports: truncnorm, parallel, stats License: GPL MD5sum: 807f006fb767881c57e3e9e1537836b7 NeedsCompilation: no File: Rsolnp_1.16_R_x86_64-pc-linux-gnu.tar.gz Package: Rsubread Version: 2.20.0 Imports: grDevices, stats, utils, Matrix License: GPL (>= 3) MD5sum: 01f640eb3cc77fc32001b09855461e06 NeedsCompilation: yes File: Rsubread_2.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: Rtpca Version: 1.16.0 Depends: R (>= 4.0.0), stats, dplyr, tidyr Imports: Biobase, methods, ggplot2, pROC, fdrtool, splines, utils, tibble Suggests: knitr, BiocStyle, TPP, testthat, rmarkdown License: GPL-3 MD5sum: db1f35229965c176411a92eb7154b8bd NeedsCompilation: no File: Rtpca_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: Rtsne Version: 0.17 Imports: Rcpp (>= 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devtools License: GPL (>= 2) MD5sum: 9fa3c7e56b96df86cbe0c86c7d61ddcd NeedsCompilation: no File: SCnorm_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: SDAMS Version: 1.26.0 Depends: R(>= 3.5), SummarizedExperiment Imports: trust, qvalue, methods, stats, utils Suggests: testthat License: GPL MD5sum: e8b5dc37daf38eb0081c36ea7c562b65 NeedsCompilation: no File: SDAMS_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: SELEX Version: 1.38.0 Depends: rJava (>= 0.5-0), Biostrings (>= 2.26.0) Imports: stats, utils License: GPL (>= 2) MD5sum: 43f7809c3ca074561497e942b6cbd0bf NeedsCompilation: no File: SELEX_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: SEtools Version: 1.20.0 Depends: R (>= 4.0), SummarizedExperiment, sechm Imports: BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR, openxlsx, pheatmap, stats, circlize, methods, sva Suggests: BiocStyle, knitr, rmarkdown, ggplot2 License: GPL MD5sum: 0998592d679f432640e7a6c545cdb11e NeedsCompilation: no File: 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Package: SICtools Version: 1.36.0 Depends: R (>= 3.0.0), methods, Rsamtools (>= 1.18.1), doParallel (>= 1.0.8), Biostrings (>= 2.32.1), stringr (>= 0.6.2), matrixStats (>= 0.10.0), plyr (>= 1.8.3), GenomicRanges (>= 1.22.4), IRanges (>= 2.4.8) Suggests: knitr, RUnit, BiocGenerics License: GPL (>= 2) MD5sum: dffe6e1d20291850252ca22bc7bee1de NeedsCompilation: yes File: SICtools_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: SIFT.Hsapiens.dbSNP132 Version: 1.0.2 Depends: VariantAnnotation, RSQLite (>= 0.11.0) Imports: AnnotationDbi License: Artistic-2.0 MD5sum: a671a647306297251ff99d09b5ca3b04 NeedsCompilation: no File: SIFT.Hsapiens.dbSNP132_1.0.2_R_x86_64-pc-linux-gnu.tar.gz Package: SIFT.Hsapiens.dbSNP137 Version: 1.0.0 Depends: VariantAnnotation (>= 1.9.15), RSQLite (>= 0.11.0) Imports: AnnotationDbi License: Artistic-2.0 MD5sum: 2263fc2f342c0edf1ec230ec401ff3d8 NeedsCompilation: no File: SIFT.Hsapiens.dbSNP137_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: SIMAT Version: 1.38.0 Depends: R 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bsseq, reshape2, data.table, ggplot2, tidyr, Suggests: BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, License: MIT + file LICENSE MD5sum: cda278bc4829288cd92a457bed673c4b NeedsCompilation: no File: SOMNiBUS_1.14.2_R_x86_64-pc-linux-gnu.tar.gz Package: SOMbrero Version: 1.4-2 Depends: R (>= 3.1.0), igraph (>= 1.0), markdown Imports: scatterplot3d, shiny, grDevices, graphics, stats, ggplot2, ggwordcloud, metR, interp, rlang Suggests: testthat, rmarkdown, knitr, hexbin, shinycssloaders, shinyBS, shinyjs, shinyjqui License: GPL (>= 2) MD5sum: ce147c03028a51b3f983a81c20d547d9 NeedsCompilation: no File: SOMbrero_1.4-2_R_x86_64-pc-linux-gnu.tar.gz Package: SPAtest Version: 3.1.2 Depends: R (>= 3.0.0) License: GPL (>= 2) MD5sum: 6795220b58369254ba97f34513ac1761 NeedsCompilation: no File: SPAtest_3.1.2_R_x86_64-pc-linux-gnu.tar.gz Package: SPEM Version: 1.46.0 Depends: R (>= 2.15.1), 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file LICENSE License_restricts_use: yes MD5sum: b8f37e15e61aa74b8dbcfa96d9196e5c NeedsCompilation: no File: SPIA_2.58.0_R_x86_64-pc-linux-gnu.tar.gz Package: SPLINTER Version: 1.32.0 Depends: R (>= 3.6.0), grDevices, stats Imports: graphics, ggplot2, seqLogo, Biostrings, pwalign, biomaRt, GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz, IRanges, S4Vectors, GenomeInfoDb, utils, plyr,stringr, methods, BSgenome.Mmusculus.UCSC.mm9, googleVis Suggests: txdbmaker, BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: 44883f77b70e8a3593773c261132c35e NeedsCompilation: no File: SPLINTER_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: SPONGE Version: 1.28.0 Depends: R (>= 3.6) Imports: Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, 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grid, httr, ica, igraph, irlba, jsonlite, KernSmooth, leidenbase, lifecycle, lmtest, MASS, Matrix (>= 1.5-0), matrixStats, miniUI, patchwork, pbapply, plotly (>= 4.9.0), png, progressr, RANN, RColorBrewer, Rcpp (>= 1.0.7), RcppAnnoy (>= 0.0.18), RcppHNSW, reticulate, rlang, ROCR, RSpectra, Rtsne, scales, scattermore (>= 1.2), sctransform (>= 0.4.1), shiny, spatstat.explore, spatstat.geom, stats, tibble, tools, utils, uwot (>= 0.1.10) LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress Suggests: ape, arrow, Biobase, BiocGenerics, BPCells, data.table, DESeq2, DelayedArray, enrichR, GenomicRanges, GenomeInfoDb, glmGamPoi, ggrastr, harmony, hdf5r, IRanges, limma, MAST, metap, mixtools, monocle, presto, rsvd, R.utils, Rfast2, rtracklayer, S4Vectors, sf (>= 1.0.0), SingleCellExperiment, SummarizedExperiment, testthat, VGAM License: MIT + file LICENSE MD5sum: 82a44ebc3ffa22cdf173416ecace69c9 NeedsCompilation: yes File: Seurat_5.2.1_R_x86_64-pc-linux-gnu.tar.gz Package: SharedObject Version: 1.20.0 Depends: R (>= 3.6.0) Imports: Rcpp, methods, stats, BiocGenerics LinkingTo: BH, Rcpp Suggests: testthat, parallel, knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 1bf0938bb72678ee205881993ba47177 NeedsCompilation: yes File: SharedObject_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: ShortRead Version: 1.64.0 Depends: BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>= 2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6) Imports: Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign, hwriter, methods, lattice, latticeExtra, LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi, knitr License: Artistic-2.0 MD5sum: d29be8363a1c50b1897ee65870a4b54d NeedsCompilation: yes File: ShortRead_1.64.0_R_x86_64-pc-linux-gnu.tar.gz Package: SiPSiC Version: 1.6.0 Depends: Matrix, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle 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testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>= 2.9.1), Rtsne License: GPL-3 MD5sum: 41a0d959ff293648e7d7fe4e347640f4 NeedsCompilation: no File: SingleCellExperiment_1.28.1_R_x86_64-pc-linux-gnu.tar.gz Package: SingleCellMultiModal Version: 1.18.0 Depends: R (>= 4.2.0), MultiAssayExperiment Imports: AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils Suggests: BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot License: Artistic-2.0 MD5sum: 9eeff64b6c6da8098dd547b8d4aa42b9 NeedsCompilation: no File: SingleCellMultiModal_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: SingleCellSignalR Version: 1.18.0 Depends: R (>= 4.0) Imports: BiocManager, circlize, limma, igraph, gplots, grDevices, edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr, foreach, multtest, scran, utils, Suggests: knitr, rmarkdown License: GPL-3 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a7994cc1b5a19f4b40be114dd0b30153 NeedsCompilation: no File: SomaticSignatures_2.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: SoupX Version: 1.6.2 Depends: R (>= 3.5.0) Imports: ggplot2, Matrix, methods, Seurat (>= 3.2.2) Suggests: knitr, rstan, DropletUtils, rmarkdown, formatR License: GPL-2 MD5sum: 828ad52da3be2b7c23c607067a7ae98b NeedsCompilation: no File: SoupX_1.6.2_R_x86_64-pc-linux-gnu.tar.gz Package: SpaNorm Version: 1.0.0 Depends: R (>= 4.4) Imports: edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran, SeuratObject, SingleCellExperiment, SpatialExperiment, stats, SummarizedExperiment, S4Vectors, utils Suggests: testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown, covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale License: GPL (>= 3) MD5sum: f6f9aa2d311672048e0419cfc9106627 NeedsCompilation: no File: SpaNorm_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpaceMarkers Version: 1.2.1 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, jsonlite, Matrix, qvalue, stats, utils, methods Suggests: data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr, RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), viridis, CoGAPS Enhances: BiocParallel License: MIT + file LICENSE MD5sum: 6911312cfc3d32a43680017c364bce14 NeedsCompilation: no File: SpaceMarkers_1.2.1_R_x86_64-pc-linux-gnu.tar.gz Package: Spaniel Version: 1.20.0 Depends: R (>= 4.0) Imports: Seurat, SingleCellExperiment, SummarizedExperiment, dplyr, methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg, magrittr, utils, S4Vectors, DropletUtils, jsonlite, png Suggests: knitr, rmarkdown, testthat, devtools License: MIT + file LICENSE MD5sum: 166f6105d7a99cdc0258d61aa3e06ffa NeedsCompilation: no File: Spaniel_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: SparseArray Version: 1.6.2 Depends: R (>= 4.3.0), methods, Matrix, BiocGenerics (>= 0.43.1), MatrixGenerics (>= 1.11.1), S4Vectors (>= 0.43.2), S4Arrays (>= 1.5.11) Imports: utils, stats, matrixStats, IRanges, XVector LinkingTo: S4Vectors, IRanges, XVector Suggests: HDF5Array, ExperimentHub, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 717d3d521112c854dfbf95cd5b3d2980 NeedsCompilation: yes File: SparseArray_1.6.2_R_x86_64-pc-linux-gnu.tar.gz Package: SparseDC Version: 0.1.17 Depends: R (>= 3.1.0) Imports: stats Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 45ed2bd25d38e043f998dd548f87095f NeedsCompilation: no File: SparseDC_0.1.17_R_x86_64-pc-linux-gnu.tar.gz Package: SparseM Version: 1.84-2 Depends: R (>= 2.15), methods Imports: graphics, stats, utils Suggests: knitr License: GPL (>= 2) MD5sum: 0a3f9baa70669391f774d6f9e6900a53 NeedsCompilation: yes File: SparseM_1.84-2_R_x86_64-pc-linux-gnu.tar.gz Package: SparseSignatures Version: 2.16.0 Depends: R (>= 4.1.0), NMF Imports: nnlasso, nnls, parallel, data.table, Biostrings, GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2, gridExtra, reshape2, RhpcBLASctl Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5, BiocStyle, testthat, knitr, License: file LICENSE MD5sum: 4fd8cee029c3476bf23d5038bed61640 NeedsCompilation: no File: SparseSignatures_2.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialCPie Version: 1.22.0 Depends: R (>= 3.6) Imports: colorspace (>= 1.3-2), data.table (>= 1.12.2), digest (>= 0.6.21), dplyr (>= 0.7.6), ggforce (>= 0.3.0), ggiraph (>= 0.5.0), ggplot2 (>= 3.0.0), ggrepel (>= 0.8.0), grid (>= 3.5.1), igraph (>= 1.2.2), lpSolve (>= 5.6.13), methods (>= 3.5.0), purrr (>= 0.2.5), readr (>= 1.1.1), rlang (>= 0.2.2), shiny (>= 1.1.0), shinycssloaders (>= 0.2.0), shinyjs (>= 1.0), shinyWidgets (>= 0.4.8), stats (>= 3.6.0), SummarizedExperiment (>= 1.10.1), tibble (>= 1.4.2), tidyr (>= 0.8.1), tidyselect (>= 0.2.4), tools (>= 3.6.0), utils (>= 3.5.0), zeallot (>= 0.1.0) Suggests: BiocStyle (>= 2.8.2), jpeg (>= 0.1-8), knitr (>= 1.20), rmarkdown (>= 1.10), testthat (>= 2.0.0) License: MIT + file LICENSE MD5sum: b8f9e475f26a4a4f64083eeea7e41098 NeedsCompilation: no File: SpatialCPie_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialDatasets Version: 1.4.0 Depends: ExperimentHub, SpatialExperiment, Imports: utils Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 6aa2a2369487f4663a59ad7aaf751416 NeedsCompilation: no File: SpatialDatasets_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialDecon Version: 1.16.0 Depends: R (>= 4.0.0) Imports: grDevices, stats, utils, graphics, SeuratObject, Biobase, GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4) Suggests: testthat, knitr, rmarkdown, qpdf, Seurat License: MIT + file LICENSE MD5sum: cb98fcf149a7680da743eeb154d1caca NeedsCompilation: no File: SpatialDecon_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialExperiment Version: 1.16.0 Depends: methods, SingleCellExperiment Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils License: GPL-3 MD5sum: 249f3ce5b2e7ab095f4cb15a371589c1 NeedsCompilation: no File: SpatialExperiment_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialExtremes Version: 2.1-0 Depends: R (>= 1.8.0) Imports: maps, fields License: GPL (>= 2) MD5sum: 497da8960c69bf21ecca1d7de292c994 NeedsCompilation: yes File: SpatialExtremes_2.1-0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialFeatureExperiment Version: 1.8.6 Depends: R (>= 4.2.0) Imports: Biobase, BiocGenerics, BiocNeighbors, BiocParallel, data.table, DropletUtils, EBImage, grDevices, lifecycle, Matrix, methods, rjson, rlang, S4Vectors, sf, sfheaders, SingleCellExperiment, SpatialExperiment, spatialreg, spdep (>= 1.1-7), SummarizedExperiment, stats, terra, utils, zeallot Suggests: arrow, BiocStyle, dplyr, knitr, RBioFormats, rhdf5, rmarkdown, scater, sfarrow, SFEData (>= 1.5.3), Seurat, SeuratObject, sparseMatrixStats, testthat (>= 3.0.0), tidyr, Voyager (>= 1.7.2), withr, xml2 License: Artistic-2.0 MD5sum: 6882d393ba4d53db4875ed10fd2ee2d7 NeedsCompilation: no File: SpatialFeatureExperiment_1.8.6_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialOmicsOverlay Version: 1.6.0 Depends: R (>= 4.1.0) Imports: S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML, scattermore, dplyr, pbapply, data.table, readxl, magick, grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats, utils, methods, ggtext, tools, RBioFormats Suggests: knitr, rmarkdown, testthat (>= 3.0.0), stringi, qpdf, pheatmap, viridis, cowplot, vdiffr, sf License: MIT MD5sum: 144b14dba11ebb6c9021e35824d2da72 NeedsCompilation: no File: SpatialOmicsOverlay_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpatialTools Version: 1.0.5 Depends: R (>= 3.0.2) Imports: spBayes (>= 0.3.0), Rcpp LinkingTo: Rcpp (>= 0.9.10), RcppArmadillo (>= 0.3.0) License: GPL (>= 2) MD5sum: 419d2f5e49d2a4640dc01f9e88a2c9c0 NeedsCompilation: yes File: SpatialTools_1.0.5_R_x86_64-pc-linux-gnu.tar.gz Package: SpeCond Version: 1.60.0 Depends: R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13), fields, hwriter (>= 1.1), RColorBrewer, methods License: LGPL (>= 2) MD5sum: 34185591621ade04510b8cf5c607b119 NeedsCompilation: no File: SpeCond_1.60.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpectraQL Version: 1.0.0 Depends: R (>= 4.4.0), ProtGenerics (>= 1.25.1) Imports: Spectra (>= 1.5.6), MsCoreUtils, methods Suggests: testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr, S4Vectors, BiocStyle, mzR License: Artistic-2.0 MD5sum: c075d49b565a5261861e46dc598067b2 NeedsCompilation: no File: SpectraQL_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: Spectra Version: 1.16.0 Depends: R (>= 4.0.0), S4Vectors, BiocParallel Imports: ProtGenerics (>= 1.37.1), methods, IRanges, MsCoreUtils (>= 1.7.5), graphics, grDevices, stats, tools, utils, fs, BiocGenerics, MetaboCoreUtils Suggests: testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0), rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick License: Artistic-2.0 MD5sum: 7f749664f547b5ab24573d3159e974c7 NeedsCompilation: no File: Spectra_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpectralTAD Version: 1.22.0 Depends: R (>= 3.6) Imports: dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel, magrittr, HiCcompare, GenomicRanges, utils Suggests: BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr License: MIT + file LICENSE MD5sum: 4b192909842541e02d08c8c2f37c443b NeedsCompilation: no File: SpectralTAD_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpikeIn Version: 1.48.0 Depends: R (>= 2.10), affy (>= 1.23.4) License: Artistic-2.0 MD5sum: 38e944333457bdbbc8953c7a2bdc43bc NeedsCompilation: no File: SpikeIn_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpliceWiz Version: 1.8.0 Depends: R (>= 3.5.0), NxtIRFdata Imports: ompBAM, methods, stats, utils, tools, parallel, scales, magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2, AnnotationHub, RSQLite, BiocFileCache, BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray, DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges, HDF5Array, htmltools, IRanges, patchwork, pheatmap, progress, plotly, R.utils, rhdf5, rtracklayer, SummarizedExperiment, S4Vectors, shiny, shinyFiles, shinyWidgets, shinydashboard, stringi, rhandsontable, DT, grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr LinkingTo: ompBAM, Rcpp, RcppProgress Suggests: knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0), DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi, fgsea, Rsubread License: MIT + file LICENSE MD5sum: 3af06bdea23031562339e4f772c04caa NeedsCompilation: yes File: SpliceWiz_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: SplicingFactory Version: 1.14.0 Depends: R (>= 4.1) Imports: SummarizedExperiment, methods, stats Suggests: testthat, knitr, rmarkdown, ggplot2, tidyr License: GPL-3 + file LICENSE MD5sum: 632a43b1f9e5353f19c66226a131cc4c NeedsCompilation: no File: SplicingFactory_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: SplicingGraphs Version: 1.46.0 Depends: GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22), Rgraphviz (>= 2.3.7) Imports: methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>= 0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb, GenomicRanges (>= 1.23.21), Rsamtools, graph Suggests: igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit License: Artistic-2.0 MD5sum: f1a8cc285773bf02364aef65614db470 NeedsCompilation: no File: SplicingGraphs_1.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpotClean Version: 1.8.0 Depends: R (>= 4.2.0), Imports: stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment, SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap, rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang Suggests: testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils, spelling License: GPL-3 MD5sum: 9a229d74002a55920fc067acaaf8561b NeedsCompilation: yes File: SpotClean_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: SpotSweeper Version: 1.2.0 Depends: R (>= 4.3.0) Imports: SpatialExperiment, SummarizedExperiment, BiocNeighbors, SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco, grDevices Suggests: knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 6522f4c266472d6a4739e5f7a147d8d4 NeedsCompilation: no File: SpotSweeper_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: StabMap Version: 1.0.0 Depends: R (>= 4.4.0), Imports: igraph, slam, BiocNeighbors, Matrix, MASS, abind, SummarizedExperiment, methods, MatrixGenerics, BiocGenerics, BiocSingular, BiocParallel Suggests: scran, scater, knitr, UpSetR, gridExtra, SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0), purrr, sparseMatrixStats License: GPL-2 MD5sum: 72a29275e1357438d79e3b3cf5738165 NeedsCompilation: no File: StabMap_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: StanHeaders Version: 2.32.10 Depends: R (>= 3.4.0) Imports: RcppParallel (>= 5.1.4) LinkingTo: RcppEigen (>= 0.3.4.0.0), RcppParallel (>= 5.1.4) Suggests: Rcpp, BH (>= 1.75.0-0), knitr (>= 1.36), rmarkdown, Matrix, methods, rstan, withr License: BSD_3_clause + file LICENSE MD5sum: 0adf8189a1d5d1c31253f783f9950648 NeedsCompilation: yes File: StanHeaders_2.32.10_R_x86_64-pc-linux-gnu.tar.gz Package: Statial Version: 1.8.0 Depends: R (>= 4.1.0) Imports: BiocParallel, spatstat.geom, concaveman, data.table, spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble, stringr, tidyselect, ggplot2, methods, stats, SummarizedExperiment, S4Vectors, plotly, purrr, ranger, magrittr, limma, SpatialExperiment, cluster, treekoR Suggests: BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR, ggsurvfit, lisaClust, survival License: GPL-3 MD5sum: 303efa06ab4081a0ef1acc1947a32910 NeedsCompilation: no File: Statial_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: Streamer Version: 1.52.0 Imports: methods, graph, RBGL, parallel, BiocGenerics Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz License: Artistic-2.0 MD5sum: def3242e27d7d9129194c97df0b7b4bb NeedsCompilation: yes File: Streamer_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: Structstrings Version: 1.22.1 Depends: R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), Biostrings (>= 2.57.2) Imports: methods, BiocGenerics, XVector, stringr, stringi, crayon, grDevices LinkingTo: IRanges, S4Vectors Suggests: testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle License: Artistic-2.0 MD5sum: 82a2cbc3bc037e3dd01e6672520678e7 NeedsCompilation: yes File: Structstrings_1.22.1_R_x86_64-pc-linux-gnu.tar.gz Package: StructuralVariantAnnotation Version: 1.22.0 Depends: GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R (>= 4.1.0) Imports: assertthat, Biostrings, pwalign, stringr, dplyr, methods, rlang, GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment, GenomeInfoDb, Suggests: ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown, tidyverse, knitr, ggbio, biovizBase, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, License: GPL-3 + file LICENSE MD5sum: f8a249a5922eae4e6ca427570d1e71e4 NeedsCompilation: no File: StructuralVariantAnnotation_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: SubCellBarCode Version: 1.22.0 Depends: R (>= 3.6) Imports: Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra, networkD3, ggrepel, graphics, stats, org.Hs.eg.db, AnnotationDbi Suggests: knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: fe774e507239e9b5b4d7a05c9e277cff NeedsCompilation: no File: SubCellBarCode_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: SummarizedExperiment Version: 1.36.0 Depends: R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3), GenomicRanges (>= 1.55.2), Biobase Imports: utils, stats, tools, Matrix, BiocGenerics (>= 0.51.3), S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), GenomeInfoDb (>= 1.13.1), S4Arrays (>= 1.1.1), DelayedArray (>= 0.31.12) Suggests: jsonlite, rhdf5, HDF5Array (>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest License: Artistic-2.0 MD5sum: a8fd8e3254aae88cfbb0f14e891d374f NeedsCompilation: no File: SummarizedExperiment_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: Summix Version: 2.12.0 Depends: R (>= 4.3) Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: c18f416cc36f08243af08555a6816e61 NeedsCompilation: no File: Summix_2.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: SuperExactTest Version: 1.1.0 Depends: grid (>= 3.1.0), methods, R (>= 3.1.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 2b186a6f329ec25242afa018de3969f1 NeedsCompilation: yes File: SuperExactTest_1.1.0_R_x86_64-pc-linux-gnu.tar.gz Package: SuperLearner Version: 2.0-29 Depends: R (>= 2.14.0), nnls, gam (>= 1.15) Imports: cvAUC, methods Suggests: arm, bartMachine, biglasso, bigmemory, caret, class, devtools, e1071, earth, gbm, genefilter, ggplot2, glmnet, ipred, KernelKnn, kernlab, knitr, lattice, LogicReg, MASS, mlbench, nloptr, nnet, party, polspline, prettydoc, quadprog, randomForest, ranger, RhpcBLASctl, ROCR, rmarkdown, rpart, SIS, speedglm, spls, sva, testthat, xgboost (>= 0.6) License: GPL-3 MD5sum: 3df072a7ac0503a645cdbff819f93751 NeedsCompilation: no File: SuperLearner_2.0-29_R_x86_64-pc-linux-gnu.tar.gz Package: SuppDists Version: 1.1-9.8 Depends: R (>= 3.3.0) Suggests: RcppZiggurat License: GPL (>= 2) MD5sum: 5a571c7aea3c0d2eda9cc3e39e691943 NeedsCompilation: yes File: SuppDists_1.1-9.8_R_x86_64-pc-linux-gnu.tar.gz Package: SurfR Version: 1.2.6 Depends: R (>= 4.3.0) Imports: httr, BiocFileCache, SPsimSeq, DESeq2, edgeR, openxlsx, stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr, tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, scales, venn, gridExtra, SummarizedExperiment, knitr, rjson, grDevices, graphics, utils Suggests: BiocStyle, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 9455691153e455881c2a24a5f06d3e10 NeedsCompilation: no File: SurfR_1.2.6_R_x86_64-pc-linux-gnu.tar.gz Package: SwathXtend Version: 2.28.0 Depends: e1071, openxlsx, VennDiagram, lattice License: GPL-2 MD5sum: 89fc8a03effb8bf75a5eb8984420cb46 NeedsCompilation: no File: SwathXtend_2.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: SynExtend Version: 1.18.0 Depends: R (>= 4.4.0), DECIPHER (>= 2.28.0) Imports: methods, Biostrings, S4Vectors, IRanges, utils, stats, parallel, graphics, grDevices, RSQLite, DBI Suggests: BiocStyle, knitr, igraph, markdown, rmarkdown License: GPL-3 MD5sum: beedf3069056721dc43299fdd529f141 NeedsCompilation: yes File: SynExtend_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: SynMut Version: 1.22.0 Imports: seqinr, methods, Biostrings, stringr, BiocGenerics Suggests: BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc, glue License: GPL-2 MD5sum: 68c4ee7e2c1bb33fb1f7bbd9c11de834 NeedsCompilation: no File: SynMut_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: TADCompare Version: 1.16.0 Depends: R (>= 4.0) Imports: dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2, tidyr, ggpubr, RColorBrewer, reshape2, cowplot Suggests: BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr, pheatmap, SpectralTAD, magick, qpdf License: MIT + file LICENSE MD5sum: b5c83df30d4e8db3eeb180cec3394f3d NeedsCompilation: no File: TADCompare_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: TAM Version: 4.2-21 Depends: R (>= 2.15.1), CDM (>= 6.4-19) Imports: graphics, methods, Rcpp, stats, utils LinkingTo: Rcpp, RcppArmadillo Suggests: coda, GPArotation, grDevices, lattice, lavaan, MASS, miceadds, mvtnorm, plyr, psych, sfsmisc, splines, WrightMap Enhances: LSAmitR License: GPL (>= 2) MD5sum: cd2d9135ae2da175f0842f52a53dec01 NeedsCompilation: yes File: TAM_4.2-21_R_x86_64-pc-linux-gnu.tar.gz Package: TAPseq Version: 1.18.0 Depends: R (>= 4.0.0) Imports: methods, GenomicAlignments, GenomicRanges, IRanges, BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome, GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel Suggests: testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer, BiocStyle License: MIT + file LICENSE MD5sum: 5258f0f7e7ded721a094b06f66c43daf NeedsCompilation: no File: TAPseq_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: TBX20BamSubset Version: 1.42.0 Depends: Rsamtools (>= 1.9.8) Imports: xtable License: LGPL MD5sum: a6540130b3d8dc488b9db13a4059a9b4 NeedsCompilation: no File: TBX20BamSubset_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: TCA Version: 1.2.1 Depends: R (>= 3.5.0) Imports: config, data.table, futile.logger, gmodels, matrixcalc, matrixStats, nloptr, parallel, pbapply, pracma, rsvd, stats, quadprog, Matrix Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 424878b8969b218598e74eee58aec1c0 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1.12.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: cc754ee0d19aa529b1e8392adb7a2d65 NeedsCompilation: no File: VAExprs_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: VAM Version: 1.1.0 Depends: R (>= 3.6.0), MASS, Matrix Imports: methods (>= 3.6.0) Suggests: Seurat (>= 4.0.0), SeuratObject (>= 4.0.0), sctransform (>= 0.3.2) License: GPL (>= 2) MD5sum: 5e0a35aaadad496827441cb59b206e2a NeedsCompilation: no File: VAM_1.1.0_R_x86_64-pc-linux-gnu.tar.gz Package: VCFArray Version: 1.22.0 Depends: R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28) Imports: tools, GenomicRanges, VariantAnnotation (>= 1.29.3), GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools Suggests: SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown License: GPL-3 MD5sum: ef8ef2f02a98dfb8dbbc406b6a19e146 NeedsCompilation: no File: VCFArray_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: VDJdive Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils LinkingTo: Rcpp Suggests: breakaway, covr, knitr, rmarkdown, testthat, BiocStyle License: Artistic-2.0 MD5sum: 5b832768ccc579a26af202ff403a74a9 NeedsCompilation: yes File: VDJdive_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: VERSO Version: 1.16.0 Depends: R (>= 4.1.0) Imports: utils, data.tree, ape, parallel, Rfast, stats Suggests: BiocGenerics, BiocStyle, testthat, knitr License: file LICENSE MD5sum: 026acd282d464b724228f7e95cb5fce4 NeedsCompilation: no File: VERSO_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: VGAM Version: 1.1-13 Depends: R (>= 4.1.0), methods, stats, stats4, splines Suggests: VGAMextra, MASS, mgcv Enhances: VGAMdata License: GPL-3 MD5sum: dfbaaa39fb9afbdd399bffdbefc398ce NeedsCompilation: yes File: VGAM_1.1-13_R_x86_64-pc-linux-gnu.tar.gz Package: VIM Version: 6.2.2 Depends: R (>= 3.5.0),colorspace,grid Imports: car, grDevices, magrittr, robustbase, stats, sp, vcd,MASS,nnet,e1071,methods,Rcpp,utils,graphics,laeken,ranger, data.table(>= 1.9.4) LinkingTo: Rcpp Suggests: dplyr, tinytest, knitr, rmarkdown, reactable, covr, withr License: GPL (>= 2) MD5sum: ebf8208d4287277eb7d4c082f079f78d NeedsCompilation: yes File: VIM_6.2.2_R_x86_64-pc-linux-gnu.tar.gz Package: VaSP Version: 1.18.0 Depends: R (>= 4.0), ballgown Imports: IRanges, GenomicRanges, S4Vectors, parallel, matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats, graphics, methods Suggests: knitr, rmarkdown License: GPL (>= 2.0) MD5sum: dd3706e2a01f4708a44d92aca62d3243 NeedsCompilation: no File: VaSP_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: VanillaICE Version: 1.68.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>= 1.27.6), SummarizedExperiment (>= 1.5.3) Imports: MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges (>= 1.14.0), oligoClasses (>= 1.31.1), foreach, matrixStats, data.table, grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools, stats, utils, BSgenome.Hsapiens.UCSC.hg18 Suggests: RUnit, human610quadv1bCrlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: LGPL-2 MD5sum: 50ffdbf2b51266cc3de754019a84581f NeedsCompilation: yes File: VanillaICE_1.68.0_R_x86_64-pc-linux-gnu.tar.gz Package: VarCon Version: 1.14.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 340fc0118e2a69c83d6f1aab60bce26e NeedsCompilation: no File: VarCon_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: VariantAnnotation Version: 1.52.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5), Rsamtools (>= 2.19.1) Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome (>= 1.47.3), GenomicFeatures (>= 1.31.3) LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons License: Artistic-2.0 MD5sum: f5f4bf50b35859aaa194bfc0b6b104c1 NeedsCompilation: yes File: VariantAnnotation_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: VariantExperiment Version: 1.20.0 Depends: R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>= 1.13.0), GenomicRanges, Imports: GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray, DelayedArray, Biostrings, IRanges Suggests: testthat, knitr, rmarkdown, markdown, BiocStyle License: GPL-3 MD5sum: 3ade3d57403b0b8c8512898cf49b7e93 NeedsCompilation: no File: VariantExperiment_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: VariantFiltering Version: 1.42.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1), VariantAnnotation (>= 1.13.29) Imports: utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6), GenomicRanges (>= 1.19.13), SummarizedExperiment, GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, GenomicScores (>= 1.0.0), Gviz, shiny, shinythemes, shinyjs, DT, shinyTree LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 License: Artistic-2.0 MD5sum: 50ae7150094b60dcf681cd126d00ad0b NeedsCompilation: yes File: VariantFiltering_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: VariantTools Version: 1.48.0 Depends: R (>= 3.5.0), S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), VariantAnnotation (>= 1.11.16), methods Imports: Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel, GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7), BiocParallel, GenomeInfoDb, BSgenome, Biobase Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: Artistic-2.0 MD5sum: bc28d6fb56a909092f3226a3bdd985bb NeedsCompilation: no File: VariantTools_1.48.0_R_x86_64-pc-linux-gnu.tar.gz Package: VegaMC Version: 3.44.0 Depends: R (>= 2.10.0), biomaRt, Biobase Imports: methods License: GPL-2 MD5sum: add1dc1eafe5ae69df156fabc0a71373 NeedsCompilation: yes File: VegaMC_3.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: VennDetail Version: 1.22.0 Imports: utils, grDevices, stats, methods, dplyr, purrr, tibble, magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger Suggests: knitr, rmarkdown, testthat, markdown License: GPL-2 MD5sum: 5d56f5a7c8dc28d4d7a3c346c6152b96 NeedsCompilation: no File: VennDetail_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: VennDiagram Version: 1.7.3 Depends: R (>= 3.5.0), grid (>= 2.14.1), futile.logger Imports: methods Suggests: testthat License: GPL-2 MD5sum: 361bd35766646bc801396dc95b0fab49 NeedsCompilation: no File: VennDiagram_1.7.3_R_x86_64-pc-linux-gnu.tar.gz Package: VisiumIO Version: 1.2.0 Depends: R (>= 4.4.0), TENxIO Imports: BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite, methods, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment Suggests: arrow, BiocStyle, knitr, rmarkdown, tinytest License: Artistic-2.0 MD5sum: 265a7e97f1d679f71e1993e32e850191 NeedsCompilation: no File: VisiumIO_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: Voyager Version: 1.8.1 Depends: R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3) Imports: BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>= 3.4.0), grDevices, grid, lifecycle, Matrix, matrixStats, memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales, scico, sf, SingleCellExperiment, SpatialExperiment, spdep, stats, SummarizedExperiment, terra, utils, zeallot Suggests: arrow, automap, BiocSingular, BiocStyle, cowplot, data.table, EBImage, ExperimentHub, ggh4x, gstat, hexbin, knitr, pheatmap, RBioFormats, rhdf5, rmarkdown, scater, scattermore, scran, sfarrow, SFEData, testthat (>= 3.0.0), vdiffr, xml2 License: Artistic-2.0 MD5sum: 21500e633ef5fac5ab9a3c876121ae12 NeedsCompilation: no File: Voyager_1.8.1_R_x86_64-pc-linux-gnu.tar.gz Package: VplotR Version: 1.16.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, GenomeInfoDb, GenomicAlignments, RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2, methods, graphics, stats Suggests: GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, testthat, covr, knitr, rmarkdown, pkgdown License: GPL (>= 3) MD5sum: ec3a87f9e61fc28d849691b66047cfa6 NeedsCompilation: no File: VplotR_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: WES.1KG.WUGSC Version: 1.38.0 License: GPL-2 MD5sum: a768a716cb90abefcd9df51c344f3119 NeedsCompilation: no File: WES.1KG.WUGSC_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: WGCNA Version: 1.73 Depends: R (>= 3.0), dynamicTreeCut (>= 1.62), fastcluster Imports: stats, grDevices, utils, matrixStats (>= 0.8.1), Hmisc, impute, splines, foreach, doParallel, preprocessCore, survival, parallel, GO.db, AnnotationDbi, Rcpp (>= 0.11.0) LinkingTo: Rcpp Suggests: org.Hs.eg.db, org.Mm.eg.db, infotheo, entropy, minet License: GPL (>= 2) MD5sum: 79a679b3db1c26af031c3d11199af8b1 NeedsCompilation: yes File: WGCNA_1.73_R_x86_64-pc-linux-gnu.tar.gz Package: WGSmapp Version: 1.18.0 Depends: R (>= 3.6.0), GenomicRanges License: GPL-2 MD5sum: 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graphics, grDevices, gtools, methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta, siggenes Suggests: MASS, RUnit Enhances: coda License: LGPL-2 MD5sum: e81e9504b7d8f739bbaafe4cbbeaf702 NeedsCompilation: yes File: XDE_2.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: XINA Version: 1.24.0 Depends: R (>= 3.5) Imports: mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools, grDevices, graphics, utils, STRINGdb Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 8315967c09e59abe035b3aa15f4df22b NeedsCompilation: no File: XINA_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: XLConnect Version: 1.2.0 Depends: R (>= 3.6.0) Imports: methods, rJava (>= 1.0-1) Suggests: RUnit, lattice, ggplot2 (>= 0.9.3), zoo License: GPL-3 MD5sum: 12868fd61a402d0bb48e05d108807f44 NeedsCompilation: no File: XLConnect_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: XML Version: 3.99-0.18 Depends: R (>= 4.0.0), methods, utils Suggests: bitops, RCurl License: BSD_3_clause + file LICENSE MD5sum: 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Version: 1.22.0 Depends: R (>= 3.6) Imports: methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2, scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid, nlme, PharmacoGx, downloader Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: e86f100f1bb9fc323453637464c2e7d5 NeedsCompilation: no File: Xeva_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 Version: 0.99.12 Depends: R (>= 2.10), BSgenome Imports: methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 License: Artistic-2.0 MD5sum: 2c393317fb58815df1fd28d0f7473b07 NeedsCompilation: no File: XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12_R_x86_64-pc-linux-gnu.tar.gz Package: XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 Version: 0.99.12 Depends: R (>= 2.10), BSgenome Imports: methods, utils, BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, BSgenome Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 License: Artistic-2.0 MD5sum: 9fcb635a62a62e3451a51bce881701eb NeedsCompilation: no File: XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12_R_x86_64-pc-linux-gnu.tar.gz Package: YAPSA Version: 1.32.0 Depends: R (>= 4.0.0), GenomicRanges, ggplot2, grid Imports: limSolve, SomaticSignatures, VariantAnnotation, GenomeInfoDb, reshape2, gridExtra, corrplot, dendextend, GetoptLong, circlize, gtrellis, doParallel, parallel, PMCMRplus, ggbeeswarm, ComplexHeatmap, KEGGREST, grDevices, Biostrings, BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: 3dbd30f339ac4a3a4db6151c94db2ab1 NeedsCompilation: no File: YAPSA_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: ZygosityPredictor Version: 1.6.0 Depends: R (>= 4.3.0) Imports: GenomicAlignments, GenomicRanges, Rsamtools, IRanges, VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble, methods, knitr, 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88e61f9492604b733ea2cf11b2b80be4 NeedsCompilation: yes File: alabaster.base_1.6.1_R_x86_64-pc-linux-gnu.tar.gz Package: alabaster.bumpy Version: 1.6.0 Depends: BumpyMatrix, alabaster.base Imports: methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges Suggests: BiocStyle, rmarkdown, knitr, testthat, jsonlite License: MIT + file LICENSE MD5sum: 5b162166b7f191b22530d08584a183cb NeedsCompilation: no File: alabaster.bumpy_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: alabaster.files Version: 1.4.0 Depends: alabaster.base, Imports: methods, S4Vectors, BiocGenerics, Rsamtools Suggests: BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings License: MIT + file LICENSE MD5sum: 057cb16ca4790d0338ecfd0f2cfeaec7 NeedsCompilation: no File: alabaster.files_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: alabaster.mae Version: 1.6.0 Depends: MultiAssayExperiment, alabaster.base Imports: methods, alabaster.se, S4Vectors, jsonlite, rhdf5 Suggests: testthat, knitr, 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alabaster.vcf_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: alabaster Version: 1.6.0 Depends: alabaster.base Imports: alabaster.matrix, alabaster.ranges, alabaster.se, alabaster.sce, alabaster.spatial, alabaster.string, alabaster.vcf, alabaster.bumpy, alabaster.mae Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 37b4cae9c4e40234c502d27fb45c235e NeedsCompilation: no File: alabaster_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: alevinQC Version: 1.22.0 Depends: R (>= 4.0) Imports: rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0), GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils, tximport (>= 1.17.4), cowplot, rlang, Rcpp LinkingTo: Rcpp Suggests: knitr, BiocStyle, testthat (>= 3.0.0), BiocManager License: MIT + file LICENSE MD5sum: e52d2173d80491587f866ae553b0e801 NeedsCompilation: yes File: alevinQC_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: alluvial Version: 0.1-2 Suggests: devtools, testthat, reshape2, knitr, rmarkdown, dplyr License: MIT + 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reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk License: GPL-3 MD5sum: cb3ac9016db0be7848e4ba18819e4ba7 NeedsCompilation: no File: basilisk.utils_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: basilisk Version: 1.18.0 Depends: reticulate Imports: utils, methods, parallel, dir.expiry, basilisk.utils (>= 1.15.1) Suggests: knitr, rmarkdown, BiocStyle, testthat, callr License: GPL-3 MD5sum: f938d97c8dd3b4eda93e112abecec0bc NeedsCompilation: no File: basilisk_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: batchelor Version: 1.22.0 Depends: SingleCellExperiment Imports: SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats, methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix, SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats, BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat LinkingTo: Rcpp Suggests: testthat, BiocStyle, knitr, rmarkdown, scran, scater, bluster, scRNAseq License: GPL-3 MD5sum: ea6c55645f63ae1367bd1f72a10b8490 NeedsCompilation: yes 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Suggests: testthat, BiocStyle, knitr, rmarkdown, rcmdcheck, BiocParallel, HDF5Array, beachmat.hdf5 License: GPL-3 MD5sum: e06a38835071699e5127dfb49d99b29f NeedsCompilation: yes File: beachmat_2.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: beadarrayExampleData Version: 1.44.0 Depends: R (>= 2.13.0), Biobase (>= 2.5.5), methods, beadarray (>= 2.0.0) License: GPL-2 MD5sum: 1435d13fae49b2dbeb422bfbe6721771 NeedsCompilation: no File: beadarrayExampleData_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: beadarray Version: 2.56.0 Depends: R (>= 2.13.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin Imports: BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr License: MIT + file LICENSE MD5sum: 5a3025abcc6e195ba2e2774d6774e931 NeedsCompilation: yes File: 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biodb_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: biomaRt Version: 2.62.1 Depends: methods Imports: utils, AnnotationDbi, progress, stringr, httr2, digest, BiocFileCache, rappdirs, xml2, curl Suggests: BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2 License: Artistic-2.0 MD5sum: 60540cbfa5d7e61c9e705c93e21a4c36 NeedsCompilation: no File: biomaRt_2.62.1_R_x86_64-pc-linux-gnu.tar.gz Package: biomartr Version: 1.0.7 Depends: R (>= 3.1.1) Imports: biomaRt, Biostrings, curl, tibble, jsonlite, data.table (>= 1.9.4), dplyr (>= 0.3.0), readr (>= 1.4.0), downloader (>= 0.3), RCurl (>= 1.95-4.5), XML (>= 3.98-1.1), httr (>= 0.6.1), stringr (>= 0.6.2), purrr, R.utils, philentropy, withr, fs Suggests: knitr (>= 1.6), rmarkdown (>= 0.3.3), devtools (>= 1.6.1), testthat, seqinr, magrittr License: GPL-2 MD5sum: 8edb4e9ff5e56e48ec53a96a377b109a NeedsCompilation: yes File: biomartr_1.0.7_R_x86_64-pc-linux-gnu.tar.gz Package: biomformat Version: 1.34.0 Depends: R (>= 3.2), methods Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5 Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) License: GPL-2 MD5sum: f16ffce7ffe50d13bf30cf3515aec055 NeedsCompilation: no File: biomformat_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: biomvRCNS Version: 1.46.0 Depends: IRanges, GenomicRanges, Gviz Imports: methods, mvtnorm Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: 89e72c9e6b5705165740e8a3d8778050 NeedsCompilation: yes File: biomvRCNS_1.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: bionetdata Version: 1.1 Depends: R (>= 2.10) License: GPL (>= 2) MD5sum: fbb23f0dda4b7e0f036e030d6b3aea47 NeedsCompilation: no File: bionetdata_1.1_R_x86_64-pc-linux-gnu.tar.gz Package: bioseq Version: 0.1.4 Depends: R (>= 3.1.0) Imports: methods, vctrs, tibble, ape, crayon, dplyr, pillar, stringi, stringr, stringdist, readr, rlang Suggests: knitr, rmarkdown, testthat (>= 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SummarizedExperiment, limma Suggests: testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) License: MIT + file LICENSE MD5sum: 4b9bec454dd1db64c4535b067a6b7152 NeedsCompilation: no File: biotmle_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: biovizBase Version: 1.54.0 Depends: R (>= 3.5.0), methods Imports: grDevices, stats, scales, Hmisc, RColorBrewer, dichromat, BiocGenerics, S4Vectors (>= 0.23.19), IRanges (>= 1.99.28), GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21), SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>= 1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4), ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8), rlang Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit License: Artistic-2.0 MD5sum: df429b2b1b9c28a4ec1194adfbc10fef NeedsCompilation: yes File: 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bnem Version: 1.14.0 Depends: R (>= 4.1) Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit License: GPL-3 MD5sum: 70625845e0d7c0f4eabe9353c5886ada NeedsCompilation: no File: bnem_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: bnlearn Version: 5.0.2 Depends: R (>= 4.4.0), methods Suggests: parallel, graph, Rgraphviz, igraph, lattice, gRbase, gRain (>= 1.3-3), Rmpfr, gmp License: GPL (>= 2) MD5sum: f8d52d0a3b224be172ba2485af02a090 NeedsCompilation: yes File: bnlearn_5.0.2_R_x86_64-pc-linux-gnu.tar.gz Package: bnstruct Version: 1.0.15 Depends: R (>= 3.5.0), bitops, igraph, methods Suggests: graph, Rgraphviz, qgraph, knitr, testthat License: GPL (>= 2) | file LICENSE MD5sum: dc831b6f2b7b37b870bb24614b5388b7 NeedsCompilation: yes File: bnstruct_1.0.15_R_x86_64-pc-linux-gnu.tar.gz Package: 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rmarkdown License: GPL-3 MD5sum: 492fd2739bdfbd0eccd0f62a8a2ac077 NeedsCompilation: no File: broom.mixed_0.2.9.6_R_x86_64-pc-linux-gnu.tar.gz Package: broom Version: 1.0.7 Depends: R (>= 3.5) Imports: backports, dplyr (>= 1.0.0), generics (>= 0.0.2), glue, lifecycle, purrr, rlang, stringr, tibble (>= 3.0.0), tidyr (>= 1.0.0) Suggests: AER, AUC, bbmle, betareg (>= 3.2-1), biglm, binGroup, boot, btergm (>= 1.10.6), car (>= 3.1-2), carData, caret, cluster, cmprsk, coda, covr, drc, e1071, emmeans, epiR, ergm (>= 3.10.4), fixest (>= 0.9.0), gam (>= 1.15), gee, geepack, ggplot2, glmnet, glmnetUtils, gmm, Hmisc, irlba, interp, joineRML, Kendall, knitr, ks, Lahman, lavaan (>= 0.6.18), leaps, lfe, lm.beta, lme4, lmodel2, lmtest (>= 0.9.38), lsmeans, maps, margins, MASS, mclust, mediation, metafor, mfx, mgcv, mlogit, modeldata, modeltests (>= 0.1.6), muhaz, multcomp, network, nnet, orcutt (>= 2.2), ordinal, plm, poLCA, psych, quantreg, rmarkdown, robust, robustbase, rsample, sandwich, spdep (>= 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Depends: R (>= 3.3.0) Imports: htmltools, magrittr, purrr, lubridate, stringr, rmarkdown, glue, jsonlite, methods Suggests: testthat, shiny, covr, knitr, markdown License: MIT + file LICENSE MD5sum: 64da3b181a8b0adbcceb5c26df7f1293 NeedsCompilation: no File: bsplus_0.1.4_R_x86_64-pc-linux-gnu.tar.gz Package: bsseqData Version: 0.44.0 Depends: R (>= 3.5.0), bsseq (>= 1.16.0) License: Artistic-2.0 MD5sum: 90a55dff06a00b9f2803f8d0908c8f1f NeedsCompilation: no File: bsseqData_0.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: bsseq Version: 1.42.0 Depends: R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5) Imports: IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, parallel, tools, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array (>= 1.19.11), rhdf5 LinkingTo: Rcpp, beachmat Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat (>= 1.5.2), batchtools License: Artistic-2.0 MD5sum: 150132409c183b0214e7dff3c84da073 NeedsCompilation: yes File: bsseq_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: bugsigdbr Version: 1.12.1 Depends: R (>= 4.1) Imports: BiocFileCache, methods, vroom, utils Suggests: BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3a3b461c7a55059377b9c43b3fe33d89 NeedsCompilation: no File: bugsigdbr_1.12.1_R_x86_64-pc-linux-gnu.tar.gz Package: bumphunter Version: 1.48.0 Depends: R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges, foreach, iterators, methods, parallel, locfit Imports: matrixStats, limma, doRNG, BiocGenerics, utils, GenomicFeatures, AnnotationDbi, stats Suggests: testthat, RUnit, doParallel, txdbmaker, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene License: Artistic-2.0 MD5sum: 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SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 1c327b0fbeb9e6329086fe3eddd51f47 NeedsCompilation: yes File: ccfindR_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: ccmap Version: 1.32.0 Imports: AnnotationDbi (>= 1.36.2), BiocManager (>= 1.30.4), ccdata (>= 1.1.2), doParallel (>= 1.0.10), data.table (>= 1.10.4), foreach (>= 1.4.3), parallel (>= 3.3.3), xgboost (>= 0.6.4), lsa (>= 0.73.1) Suggests: crossmeta, knitr, rmarkdown, testthat, lydata License: MIT + file LICENSE MD5sum: 0d9b740b72d530f953db929a5eb69c19 NeedsCompilation: no File: ccmap_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: ccrepe Version: 1.42.0 Imports: infotheo (>= 1.1) Suggests: knitr, BiocStyle, BiocGenerics, testthat, RUnit License: MIT + file LICENSE MD5sum: e889861a1574823c9d8f4f6abffed52d NeedsCompilation: no File: ccrepe_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: ceRNAnetsim Version: 1.18.0 Depends: R (>= 4.0.0), dplyr, tidygraph Imports: furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats Suggests: knitr, png, rmarkdown, testthat, covr License: GPL (>= 3.0) MD5sum: 84d1b3d938e0b1bdb5a2eab5f2ce931f NeedsCompilation: no File: ceRNAnetsim_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: celaref Version: 1.24.0 Depends: R (>= 3.5.0), SummarizedExperiment Imports: MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang, BiocGenerics, S4Vectors, readr, tibble, DelayedArray Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub, testthat License: GPL-3 MD5sum: 700551f2f07ef02242d66a0ac8ab8c74 NeedsCompilation: no File: celaref_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: celda Version: 1.22.1 Depends: R (>= 4.0), SingleCellExperiment, Matrix Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot, enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne, withr, scater (>= 1.14.4), scran, dbscan, DelayedArray, stringr, ComplexHeatmap, gridExtra, circlize, dendextend, ggdendro, pROC LinkingTo: Rcpp, RcppEigen Suggests: testthat, knitr, roxygen2, rmarkdown, biomaRt, covr, BiocManager, BiocStyle, TENxPBMCData, singleCellTK, M3DExampleData License: MIT + file LICENSE MD5sum: e4a42df793385e16bc5a5bfd427f6aa7 NeedsCompilation: yes File: celda_1.22.1_R_x86_64-pc-linux-gnu.tar.gz Package: celestial Version: 1.4.6 Depends: R (>= 3.00), RANN, NISTunits, pracma License: GPL-3 MD5sum: badcb300e353e7a2da07dd09c192744a NeedsCompilation: no File: celestial_1.4.6_R_x86_64-pc-linux-gnu.tar.gz Package: cellbaseR Version: 1.30.0 Depends: R(>= 3.4) Imports: methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils, Rsamtools, BiocParallel, foreach, utils, parallel, doParallel Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation License: Apache License (== 2.0) MD5sum: 50f450aa792444c4f9baf151c5058b81 NeedsCompilation: no File: cellbaseR_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: celldex Version: 1.16.0 Depends: SummarizedExperiment Imports: utils, methods, Matrix, ExperimentHub, AnnotationHub, AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats, gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI, RSQLite, jsonlite Suggests: testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate, BiocManager, ensembldb License: GPL-3 MD5sum: 16f48c2968c62cd1d100e61729533860 NeedsCompilation: no File: celldex_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: cellity Version: 1.34.0 Depends: R (>= 3.3) Imports: AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid, mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats, topGO, utils Suggests: BiocStyle, caret, knitr, testthat, rmarkdown License: GPL (>= 2) MD5sum: 8490bd00f5a0b5c63db79c3ca534b5b2 NeedsCompilation: no File: cellity_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: cellmigRation Version: 1.14.0 Depends: R (>= 4.1), methods, foreach Imports: tiff, graphics, stats, utils, reshape2, parallel, doParallel, grDevices, matrixStats, FME, SpatialTools, sp, vioplot, FactoMineR, Hmisc Suggests: knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics, BiocManager, kableExtra, rgl License: GPL-2 MD5sum: 36a4643cc7b09fb6604add78547eb2a9 NeedsCompilation: no File: cellmigRation_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: cellranger Version: 1.1.0 Depends: R (>= 3.0.0) Imports: rematch, tibble Suggests: covr, testthat (>= 1.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 0cba8ac52187efe493bdb8a7e158d243 NeedsCompilation: no File: cellranger_1.1.0_R_x86_64-pc-linux-gnu.tar.gz Package: cellscape Version: 1.30.0 Depends: R (>= 3.3) Imports: dplyr (>= 0.4.3), gtools (>= 3.5.0), htmlwidgets (>= 0.5), jsonlite (>= 0.9.19), reshape2 (>= 1.4.1), stringr (>= 1.0.0) Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 818c2816c5725fbfefddb5845af3f45e NeedsCompilation: no File: cellscape_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: cellxgenedp Version: 1.10.0 Depends: dplyr Imports: httr, curl, utils, tools, cli, shiny, DT, rjsoncons Suggests: zellkonverter, SingleCellExperiment, HDF5Array, tidyr, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery License: Artistic-2.0 MD5sum: 83e9f6c066765f387c99f1cd14566505 NeedsCompilation: no File: cellxgenedp_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: censcyt Version: 1.14.0 Depends: R (>= 4.0), diffcyt Imports: BiocParallel, broom.mixed, dirmult, dplyr, edgeR, fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp, purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment, survival, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 License: MIT + file LICENSE MD5sum: bf39dcc648f882de1c85160817e4eaec NeedsCompilation: no File: censcyt_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: cfDNAPro Version: 1.12.0 Depends: R (>= 4.1.0), magrittr (>= 1.5.0) Imports: tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools (>= 2.4.0), rlang (>= 0.4.0), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38 Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat License: GPL-3 MD5sum: 6231b28a5a332c6c61bb9baef5e03a9d NeedsCompilation: no File: cfDNAPro_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: cfToolsData Version: 1.4.0 Depends: R (>= 4.3.0) Imports: utils, ExperimentHub Suggests: BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0) License: file LICENSE MD5sum: 68a532c755d0e37775f1d05e7a63fb17 NeedsCompilation: no File: cfToolsData_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: cfTools Version: 1.6.0 Imports: Rcpp, utils, GenomicRanges, basilisk, R.utils, stats, cfToolsData LinkingTo: Rcpp, BH Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: file LICENSE MD5sum: 5a3d3b44b6bf1b4fa392461fc7d7a874 NeedsCompilation: yes File: cfTools_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: cfdnakit Version: 1.4.0 Depends: R (>= 4.3) Imports: Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang Suggests: rmarkdown, knitr, roxygen2, BiocStyle License: GPL-3 MD5sum: f3c86192292c11ff2713eb46a616950f NeedsCompilation: no File: cfdnakit_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: cghMCR Version: 1.64.0 Depends: methods, DNAcopy, CNTools, limma Imports: BiocGenerics (>= 0.1.6), stats4 License: LGPL MD5sum: e72c0eb44e8a8847b4c2eb888508dc3e NeedsCompilation: no File: cghMCR_1.64.0_R_x86_64-pc-linux-gnu.tar.gz Package: changepoint.np Version: 1.0.5 Depends: changepoint Imports: methods,zoo,Rdpack License: GPL MD5sum: 0e8f2be60a4d4dbc6aa6f0a9cecfc56e NeedsCompilation: yes File: changepoint.np_1.0.5_R_x86_64-pc-linux-gnu.tar.gz Package: changepoint Version: 2.3 Depends: R(>= 3.2), methods, stats, zoo(>= 0.9-1) Suggests: testthat, vdiffr License: GPL MD5sum: 32174a4cc1050ccde3f758052117ea4d NeedsCompilation: yes File: changepoint_2.3_R_x86_64-pc-linux-gnu.tar.gz Package: checkmate Version: 2.3.2 Depends: R (>= 3.0.0) Imports: backports (>= 1.1.0), utils Suggests: R6, fastmatch, data.table (>= 1.9.8), devtools, ggplot2, knitr, magrittr, microbenchmark, rmarkdown, testthat (>= 3.0.4), tinytest (>= 1.1.0), tibble License: BSD_3_clause + file LICENSE MD5sum: 32666b275574ae146aa8d1811c3ef158 NeedsCompilation: yes File: checkmate_2.3.2_R_x86_64-pc-linux-gnu.tar.gz Package: chemometrics Version: 1.4.4 Depends: R (>= 2.10), rpart Imports: class, e1071, MASS, nnet, pcaPP, robustbase, som, lars, pls, mclust Suggests: gclus License: GPL (>= 3) MD5sum: fd6b98f94a718a25791d000908f72773 NeedsCompilation: no File: chemometrics_1.4.4_R_x86_64-pc-linux-gnu.tar.gz Package: chihaya Version: 1.6.0 Depends: DelayedArray Imports: methods, Matrix, rhdf5, Rcpp, HDF5Array LinkingTo: Rcpp, Rhdf5lib Suggests: BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix, BiocStyle, testthat, rmarkdown, knitr License: GPL-3 MD5sum: c4b7c9ec32f9d9bd4183d668d7b1d392 NeedsCompilation: yes File: chihaya_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: chimeraviz Version: 1.32.0 Depends: Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors, ensembldb, AnnotationFilter, data.table Imports: methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments, RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db, org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr, BiocStyle, checkmate, gtools, magick Suggests: testthat, roxygen2, devtools, knitr, lintr License: Artistic-2.0 MD5sum: 297e17fb1214b8af01fd0d5fda315ad9 NeedsCompilation: no File: chimeraviz_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: chipenrich.data Version: 2.30.0 Depends: R (>= 3.5.0) Imports: AnnotationDbi, BiocGenerics, methods, GenomicRanges, GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene License: GPL-3 MD5sum: be0c62d9c70c653fc6de5266958a2157 NeedsCompilation: no File: chipenrich.data_2.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: chipenrich Version: 2.30.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra, MASS, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms, rtracklayer, S4Vectors (>= 0.23.10), stats, stringr, utils Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat License: GPL-3 MD5sum: 30e6fb654960bfae80e5d31bbb8899ed NeedsCompilation: no File: chipenrich_2.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: chipseq Version: 1.56.0 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8), ShortRead Imports: methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges, ShortRead Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene, BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr License: Artistic-2.0 MD5sum: b41e2d4d5d58d22b57eedb653cf24b6e NeedsCompilation: yes File: chipseq_1.56.0_R_x86_64-pc-linux-gnu.tar.gz Package: chk Version: 0.10.0 Depends: R (>= 3.6) Imports: lifecycle, methods, rlang, tools Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0), withr License: MIT + file LICENSE MD5sum: 316168b717ee52e17f5bd371f312ebb2 NeedsCompilation: no File: chk_0.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: chopsticks Version: 1.72.0 Imports: graphics, stats, utils, methods, survival Suggests: hexbin License: GPL-3 MD5sum: 9e8afe98a6fb390ff715237c40226523 NeedsCompilation: yes File: chopsticks_1.72.0_R_x86_64-pc-linux-gnu.tar.gz Package: chromDraw Version: 2.36.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: fedd571259d07b39e694216cc6cc28ab NeedsCompilation: yes File: chromDraw_2.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: chromPlot Version: 1.34.0 Depends: stats, utils, graphics, grDevices, datasets, base, biomaRt, GenomicRanges, R (>= 3.1.0) Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene License: GPL (>= 2) MD5sum: c65a840d0a6d6ace58861291dc9201cc NeedsCompilation: no File: chromPlot_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: chromVAR Version: 1.28.0 Depends: R (>= 3.5.0) Imports: IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor, BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment, RColorBrewer, BSgenome LinkingTo: Rcpp, RcppArmadillo Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr License: MIT + file LICENSE MD5sum: 9e7302015e4c715884b454d55db82937 NeedsCompilation: yes File: chromVAR_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: chromhmmData Version: 0.99.2 Depends: R (>= 4.1) Suggests: rmarkdown, knitr License: GPL-3 MD5sum: 29df868e0f9cb235ad9a5c2ea2e96993 NeedsCompilation: no File: chromhmmData_0.99.2_R_x86_64-pc-linux-gnu.tar.gz Package: chromote Version: 0.4.0 Imports: curl, fastmap, jsonlite, later (>= 1.1.0), magrittr, processx, promises (>= 1.1.1), R6, rlang, utils, websocket (>= 1.2.0) Suggests: showimage, testthat (>= 3.0.0) License: GPL-2 MD5sum: c8bfec5777aa553f05e2aab34da553ad NeedsCompilation: no File: 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Imports: dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2, edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2, ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb, universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, Biostrings, gwascat, BSgenome, Suggests: testthat, knitr, roxygen2, rmarkdown, devtools, gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BiocManager, License: GPL-3 MD5sum: a67a5c3f681eca291d198425d64d3d02 NeedsCompilation: no File: circRNAprofiler_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: circlize Version: 0.4.16 Depends: R (>= 4.0.0), graphics Imports: GlobalOptions (>= 0.1.2), shape, grDevices, utils, stats, colorspace, methods, grid Suggests: knitr, dendextend (>= 1.0.1), ComplexHeatmap (>= 2.0.0), gridBase, png, markdown, bezier, covr, rmarkdown License: MIT + file LICENSE MD5sum: ff1ed90e2aa461af1b7868a6ede37288 NeedsCompilation: no File: 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apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: c6e999750bf6e28bad48f0f1a8151ce1 NeedsCompilation: no File: cogena_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: cogeqc Version: 1.10.0 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings Suggests: testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle, rmarkdown, covr License: GPL-3 MD5sum: d214a0e67f4a2187f130b1cb495a2eb5 NeedsCompilation: no File: cogeqc_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: coin Version: 1.4-3 Depends: R (>= 3.6.0), survival Imports: methods, parallel, stats, stats4, utils, libcoin (>= 1.0-9), matrixStats (>= 0.54.0), modeltools (>= 0.2-9), mvtnorm (>= 1.0-5), multcomp LinkingTo: libcoin (>= 1.0-9) Suggests: xtable, e1071, vcd, TH.data (>= 1.0-7) License: GPL-2 MD5sum: 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RcppArmadillo Suggests: knitr, formatR, rmarkdown, viridis License: LGPL-3 | file LICENSE MD5sum: be735df87e6018fd1c49bf7a21086736 NeedsCompilation: yes File: cytometree_2.0.2_R_x86_64-pc-linux-gnu.tar.gz Package: cytoviewer Version: 1.6.0 Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, markdown, testthat License: GPL-3 MD5sum: 9bcf64cb06e61cbb6d618d00d94e2ccb NeedsCompilation: no File: cytoviewer_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: dStruct Version: 1.12.0 Depends: R (>= 4.1) Imports: zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors, rlang, grDevices, stats, utils Suggests: BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: f665ae71659b09e2a567c1f37746940b NeedsCompilation: no File: dStruct_1.12.0_R_x86_64-pc-linux-gnu.tar.gz 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dagLogo_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: dagitty Version: 0.3-4 Depends: R (>= 3.0.0) Imports: V8, jsonlite, boot, MASS, methods, grDevices, stats, utils, graphics Suggests: igraph, knitr, base64enc (>= 0.1-3), testthat, markdown, rmarkdown, lavaan, CCP, fastDummies License: GPL-2 MD5sum: 7450cbb278a6ef41ceb61c65d47a0c07 NeedsCompilation: no File: dagitty_0.3-4_R_x86_64-pc-linux-gnu.tar.gz Package: dar Version: 1.2.0 Depends: R (>= 4.4.0) Imports: cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue, gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr, readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr, UpSetR, waldo Suggests: ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr, DESeq2, devtools, furrr, future, knitr, lefser, limma, Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2, roxyglobals, roxytest, rstatix, SummarizedExperiment, TreeSummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 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BiocStyle, formatR, cowplot, ggplotify, dagitty, lmtest, sandwich, devtools, curatedTCGAData, TCGAutils, SummarizedExperiment, RcppParallel, docopt, CARNIVAL License: GPL-3 MD5sum: 9d58f9923356466cbccd953bcaa40dbe NeedsCompilation: no File: dce_1.13.0_R_x86_64-pc-linux-gnu.tar.gz Package: ddCt Version: 1.62.0 Depends: R (>= 2.3.0), methods Imports: Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice, BiocGenerics Suggests: testthat (>= 3.0.0), RUnit License: LGPL-3 MD5sum: 96e526aed58a192c2ce7d93c3b4e98b3 NeedsCompilation: no File: ddCt_1.62.0_R_x86_64-pc-linux-gnu.tar.gz Package: deSolve Version: 1.40 Depends: R (>= 3.3.0) Imports: methods, graphics, grDevices, stats Suggests: scatterplot3d, FME License: GPL (>= 2) MD5sum: d88ab4eb1fd9d1667ec79fb0f16e2128 NeedsCompilation: yes File: deSolve_1.40_R_x86_64-pc-linux-gnu.tar.gz Package: dearseq Version: 1.18.0 Depends: R (>= 3.6.0) Imports: CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr, matrixStats, methods, patchwork, 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SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr, tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW, smoother, scales, scatterplot3d LinkingTo: Rcpp, RcppEigen, grDevices Suggests: knitr, rmarkdown, igraph, testthat, FNN, tidyverse, gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq, org.Mm.eg.db, scran, repr Enhances: rgl, SingleCellExperiment License: GPL-3 MD5sum: 7f2f01e4652ce00643bd4693ab8349c1 NeedsCompilation: yes File: destiny_3.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: detectseparation Version: 0.3 Depends: R (>= 3.3.0) Imports: ROI, ROI.plugin.lpsolve, lpSolveAPI, pkgload Suggests: knitr, rmarkdown, covr, brglm2, AER, tinytest, ROI.plugin.ecos, ROI.plugin.glpk, ROI.plugin.alabama, ROI.plugin.neos License: GPL-3 MD5sum: c70de178a1eff972cbb5bf61f0fc4246 NeedsCompilation: no File: detectseparation_0.3_R_x86_64-pc-linux-gnu.tar.gz Package: dgof Version: 1.5.1 License: GPL (>= 2.0) MD5sum: 68581359c72b91addd4132f19b1b47f2 NeedsCompilation: yes File: 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rtracklayer, ComplexHeatmap, ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr, matrixStats, IRanges, ensembldb, viridisLite Suggests: BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: fad6024d2dcfd9be03e750c9bf0ead36 NeedsCompilation: no File: diffUTR_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: diffcoexp Version: 1.26.0 Depends: R (>= 3.5), WGCNA, SummarizedExperiment Imports: stats, DiffCorr, psych, igraph, BiocGenerics Suggests: GEOquery, RUnit License: GPL (> 2) MD5sum: ba426706985940529d6963991928b315 NeedsCompilation: no File: diffcoexp_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: diffcyt Version: 1.26.1 Depends: R (>= 3.4.0) Imports: flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma, edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats, methods, utils, grDevices, graphics, ComplexHeatmap, circlize, grid Suggests: BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST License: MIT + file LICENSE MD5sum: ed072187735722f4b843f9575ca7bd84 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stats, biwt, gtools, MASS, tools, dplyr, methods, utils LinkingTo: Rcpp Suggests: BiocStyle, knitr, testthat (>= 3.0.0) License: GPL-3 MD5sum: bcaa2fa25f8e94eb18f8ac701bc4cbbc NeedsCompilation: yes File: discordant_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: distances Version: 0.1.11 Depends: R (>= 3.4.0) Imports: stats Suggests: testthat License: GPL (>= 3) MD5sum: 44ae06b227b6a10d95f45923fec12848 NeedsCompilation: yes File: distances_0.1.11_R_x86_64-pc-linux-gnu.tar.gz Package: distill Version: 1.6 Imports: base64enc, bookdown (>= 0.8), digest, downlit (>= 0.4.1), htmltools, jsonlite (>= 1.3), knitr (>= 1.15.6), lubridate (>= 1.7.10), mime, openssl, png, rmarkdown (>= 2.11), rprojroot, rstudioapi, stats, stringr, tools, utils, whisker, xfun (>= 0.18), xml2, yaml Suggests: covr, DiagrammeR, htmlwidgets, progress, r2d3, rsconnect, shiny, testthat (>= 3.0.0), withr License: Apache License 2.0 MD5sum: f89b559486c4d81402031141b7eca0e8 NeedsCompilation: no File: 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rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran License: MIT + file LICENSE MD5sum: 9bd20ff5d3f509afc41f3c158c974eab NeedsCompilation: no File: dittoSeq_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: divergence Version: 1.22.0 Depends: R (>= 3.6), SummarizedExperiment Suggests: knitr, rmarkdown License: GPL-2 MD5sum: 58c4243f8f2d2530556324085bbfc4dc NeedsCompilation: no File: divergence_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: dixonTest Version: 1.0.4 License: GPL-3 MD5sum: fa5fc5d571dc990378756e0e56bb0683 NeedsCompilation: yes File: dixonTest_1.0.4_R_x86_64-pc-linux-gnu.tar.gz Package: dks Version: 1.52.0 Depends: R (>= 2.8) Imports: cubature License: GPL MD5sum: f15197be62e015ab9274908e9ec78d1e NeedsCompilation: no File: dks_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: dlstats Version: 0.1.7 Depends: R (>= 3.3.0) Imports: ggplot2, jsonlite, magrittr, RColorBrewer, scales, utils Suggests: knitr, tidyr, DT, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 5138269a7182231b359f3d2da714aac4 NeedsCompilation: no File: dlstats_0.1.7_R_x86_64-pc-linux-gnu.tar.gz Package: dml Version: 1.1.0 Depends: MASS Imports: lfda Suggests: testthat License: MIT + file LICENSE MD5sum: e0bd7a87bbb54a8108d48526e76289fd NeedsCompilation: no File: dml_1.1.0_R_x86_64-pc-linux-gnu.tar.gz Package: dmrseq Version: 1.26.0 Depends: R (>= 3.5), bsseq Imports: GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer, bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats, BiocParallel, outliers, methods, locfit, IRanges, grDevices, graphics, stats, utils, annotatr, AnnotationHub, rtracklayer, GenomeInfoDb, splines Suggests: knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: MIT + file LICENSE MD5sum: 5005802d403f95df6a7847885fa5db0b NeedsCompilation: no File: dmrseq_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: doBy Version: 4.6.25 Depends: R (>= 4.2.0), methods Imports: boot, broom, cowplot, Deriv, dplyr, ggplot2, MASS, Matrix, modelr, microbenchmark, rlang, tibble, tidyr, Suggests: geepack, knitr, lme4, markdown, multcomp, pbkrtest (>= 0.5.2), survival, testthat (>= 2.1.0) License: GPL (>= 2) MD5sum: 3fff0ed4b2f4f8b84ee960c825f452c9 NeedsCompilation: no File: doBy_4.6.25_R_x86_64-pc-linux-gnu.tar.gz Package: doFuture Version: 1.0.1 Depends: foreach (>= 1.5.0), future (>= 1.32.0) Imports: future.apply, globals, iterators, parallel, utils Suggests: doRNG (>= 1.8.2), markdown, R.rsp License: LGPL (>= 2.1) MD5sum: f97b9dd2083d1ba6b676eb9a428814d8 NeedsCompilation: no File: doFuture_1.0.1_R_x86_64-pc-linux-gnu.tar.gz Package: doMC Version: 1.3.8 Depends: R (>= 2.14.0), foreach(>= 1.2.0), iterators(>= 1.0.0), parallel Imports: utils Enhances: compiler, RUnit License: GPL-2 OS_type: unix MD5sum: 354394cbe26ada5860c5786c02dad89c NeedsCompilation: no File: doMC_1.3.8_R_x86_64-pc-linux-gnu.tar.gz Package: doParallel Version: 1.0.17 Depends: R (>= 2.14.0), foreach (>= 1.2.0), iterators (>= 1.0.0), parallel, utils Suggests: caret, mlbench, rpart, RUnit Enhances: compiler License: GPL-2 MD5sum: 1b1e9e8fb871ff96f0ddd503d38c1489 NeedsCompilation: no File: doParallel_1.0.17_R_x86_64-pc-linux-gnu.tar.gz Package: doRNG Version: 1.8.6.1 Depends: R (>= 3.0.0), foreach, rngtools (>= 1.5) Imports: stats, utils, iterators Suggests: doParallel, doMPI, doRedis, rbenchmark, devtools, knitr, rbibutils (>= 1.3), testthat, pkgmaker (>= 0.32.7), covr License: GPL (>= 2) MD5sum: 42a4381fbd73a5f1d988982c04b00ee1 NeedsCompilation: no File: doRNG_1.8.6.1_R_x86_64-pc-linux-gnu.tar.gz Package: doSNOW Version: 1.0.20 Depends: R (>= 2.5.0), foreach(>= 1.2.0), iterators(>= 1.0.0), snow(>= 0.3.0), utils Suggests: compiler, RUnit, caret, mlbench, rpart, parallel License: GPL-2 MD5sum: e3d4fd79eba1f48bfa33d6e83b9a092d NeedsCompilation: no File: doSNOW_1.0.20_R_x86_64-pc-linux-gnu.tar.gz Package: dominoSignal Version: 1.0.0 Depends: R(>= 4.2.0), Imports: biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid, igraph, Matrix, methods, plyr, stats, utils Suggests: knitr, patchwork, rmarkdown, Seurat, testthat, formatR, BiocFileCache, SingleCellExperiment License: GPL-3 | file LICENSE MD5sum: 92fe125ec507886bb734394272bf1cb4 NeedsCompilation: no File: dominoSignal_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: doppelgangR Version: 1.34.0 Depends: R (>= 3.5.0), Biobase, BiocParallel Imports: sva, impute, digest, mnormt, methods, grDevices, graphics, stats, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat License: GPL (>= 2.0) MD5sum: 72b099ae4415876c24299a17d964a09d NeedsCompilation: no File: doppelgangR_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: dorothea Version: 1.18.0 Depends: R (>= 4.0) Imports: dplyr, magrittr, bcellViper, decoupleR, Suggests: Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils License: GPL-3 + file LICENSE 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Package: enrichR Version: 3.4 Depends: R (>= 3.5.0) Imports: httr, curl, rjson, ggplot2, WriteXLS Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 2695e71a36f25b909779cfc88c8199d4 NeedsCompilation: no File: enrichR_3.4_R_x86_64-pc-linux-gnu.tar.gz Package: enrichViewNet Version: 1.4.0 Depends: R (>= 4.2.0) Imports: gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE, methods Suggests: BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick License: Artistic-2.0 MD5sum: f1d105489c1ba31ebcca250811e9eb4c NeedsCompilation: no File: enrichViewNet_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: enrichplot Version: 1.26.6 Depends: R (>= 3.5.0) Imports: aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7), ggnewscale, ggplot2, ggrepel (>= 0.9.0), ggtangle (>= 0.0.4), graphics, grid, igraph, methods, plyr, purrr, RColorBrewer, reshape2, rlang, stats, utils, scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6) Suggests: clusterProfiler, dplyr, europepmc, ggarchery, ggupset, knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges, grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr License: Artistic-2.0 MD5sum: b0e73f69db6f25a8395aa0a45b934022 NeedsCompilation: no File: enrichplot_1.26.6_R_x86_64-pc-linux-gnu.tar.gz Package: ensembldb Version: 2.30.0 Depends: R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18), GenomicFeatures (>= 1.49.6), AnnotationFilter (>= 1.5.2) Imports: methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb, AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>= 0.23.10), Rsamtools, IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9), curl Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), rmarkdown, AnnotationHub Enhances: RMariaDB, shiny License: LGPL MD5sum: cf500370467fd5161ee9a12892af30a9 NeedsCompilation: no File: 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MASS (>= 3.1-20), dplyr, foreign, ggplot2, knitr, rmarkdown, plyr, RColorBrewer, scales, sp, spData (>= 2.3.0), spatstat, tidyr License: GPL (>= 2) MD5sum: 50219e1543974eb3bf099fd39443915c NeedsCompilation: no File: epiR_2.0.80_R_x86_64-pc-linux-gnu.tar.gz Package: epialleleR Version: 1.14.0 Depends: R (>= 4.1) Imports: stats, methods, utils, data.table, BiocGenerics, GenomicRanges, Rcpp LinkingTo: Rcpp, BH, Rhtslib Suggests: GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit, knitr, rmarkdown, ggplot2 License: Artistic-2.0 MD5sum: 98bf333a9c2a14055c05aada3a985e07 NeedsCompilation: yes File: epialleleR_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: epidecodeR Version: 1.14.0 Depends: R (>= 3.1.0) Imports: EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges, rstatix, ggpubr, methods, stats, utils, dplyr Suggests: knitr, rmarkdown License: GPL-3 MD5sum: 66aa6585620f906d050f948be7334ebf NeedsCompilation: no File: epidecodeR_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: epigenomix Version: 1.46.0 Depends: R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment Imports: BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb, beadarray License: LGPL-3 MD5sum: 77b99ed2ddaaafe3684b3b295e4bd189 NeedsCompilation: no File: epigenomix_1.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: epigraHMM Version: 1.14.0 Depends: R (>= 3.5.0) Imports: Rcpp, magrittr, data.table, SummarizedExperiment, methods, GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools, bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5, Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap, grDevices LinkingTo: Rcpp, RcppArmadillo, Rhdf5lib Suggests: testthat, knitr, rmarkdown, BiocStyle, BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData License: MIT + file LICENSE MD5sum: 99b76977b2490fadd66582d9bc03acb8 NeedsCompilation: yes File: epigraHMM_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: epimutacionsData Version: 1.10.0 Depends: R (>= 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grDevices License: MIT + file LICENSE MD5sum: 4a515b86462ba7820c993f88f9dfbcc0 NeedsCompilation: yes File: epimutacions_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: epiregulon.extra Version: 1.2.0 Depends: R (>= 4.4), SingleCellExperiment Imports: scran, ComplexHeatmap, Matrix, SummarizedExperiment, checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph, lifecycle, patchwork, reshape2, scales, scater, stats Suggests: epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome, S4Vectors, scuttle, vdiffr, ggrastr, ggrepel License: MIT + file LICENSE MD5sum: b8063d6788ac10f55134a45e76a1d7b4 NeedsCompilation: no File: epiregulon.extra_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: epiregulon Version: 1.2.0 Depends: R (>= 4.4), SingleCellExperiment Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp, S4Vectors, SummarizedExperiment, bluster, checkmate, entropy, lifecycle, methods, scran, scuttle, stats, utils, scMultiome, GenomeInfoDb, GenomicRanges, AUCell, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat LinkingTo: Rcpp, beachmat, assorthead Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0), coin, scater, beachmat.hdf5 License: MIT + file LICENSE MD5sum: c26291d39206ac5014648472798203e4 NeedsCompilation: yes File: epiregulon_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: epistack Version: 1.12.0 Depends: R (>= 4.1) Imports: GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors, IRanges, graphics, plotrix, grDevices, stats, methods Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick License: MIT + file LICENSE MD5sum: b680efdd72ed62d7f29f4eb6f779698d NeedsCompilation: no File: epistack_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: epistasisGA Version: 1.8.0 Depends: R (>= 4.2) Imports: BiocParallel, data.table, matrixStats, stats, survival, igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid, bigmemory, graphics, utils LinkingTo: Rcpp, RcppArmadillo, BH, bigmemory Suggests: BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat (>= 3.0.0) License: GPL-3 MD5sum: ee6d8dc3a3feb4a6d2a969b9871e8e00 NeedsCompilation: yes File: epistasisGA_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: epivizrChart Version: 1.28.0 Depends: R (>= 3.5.0) Imports: epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson, methods, BiocGenerics Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub License: Artistic-2.0 MD5sum: 177737be79c0819e3358995f68bd6d32 NeedsCompilation: no File: epivizrChart_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: epivizrData Version: 1.34.0 Depends: R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase Imports: S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0), OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI, matrixStats License: MIT + file LICENSE MD5sum: 9a6c48dc9b13cdefb94b9cd67dcc7b83 NeedsCompilation: no File: epivizrData_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: epivizrServer Version: 1.34.0 Depends: R (>= 3.2.3), methods Imports: httpuv (>= 1.3.0), R6 (>= 2.0.0), rjson, mime (>= 0.2) Suggests: testthat, knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: f39028ad1c9f0ca1fb40eb321f613570 NeedsCompilation: no File: epivizrServer_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: epivizrStandalone Version: 1.34.0 Depends: R (>= 3.2.3), epivizr (>= 2.3.6), methods Imports: git2r, epivizrServer, GenomeInfoDb, BiocGenerics, GenomicFeatures, S4Vectors Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle License: MIT + file LICENSE MD5sum: fec4e1a95f2a7ff1929e9e5a8ebddb74 NeedsCompilation: no File: epivizrStandalone_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: epivizr Version: 2.36.0 Depends: R (>= 3.5.0), methods Imports: epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4), GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, minfi, rmarkdown License: Artistic-2.0 MD5sum: 232ff2eb2073ecdc7a7be723dabc9823 NeedsCompilation: no File: epivizr_2.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: erccdashboard Version: 1.40.0 Depends: R (>= 4.0), ggplot2 (>= 2.1.0), gridExtra (>= 2.0.0) Imports: edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr, qvalue, reshape2, ROCR, scales, stringr, knitr Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 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JASPAR2018, TFBSTools, grDevices, graphics, stats, utils, parallel, corrplot, BiocManager, motifmatchr LinkingTo: Rcpp Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat, webshot, prettydoc License: GPL-3 | file LICENSE Archs: x64 MD5sum: 27103344e5f5a512edd0e977b52c60af NeedsCompilation: yes File: esATAC_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: escape Version: 2.2.3 Depends: R (>= 4.1) Imports: AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2, ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges, msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils, SummarizedExperiment, UCell, stringr, methods, SeuratObject, Matrix Suggests: Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle, RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 4251a7a948d49f45e86ca78728bda896 NeedsCompilation: no File: escape_2.2.3_R_x86_64-pc-linux-gnu.tar.gz Package: escheR Version: 1.6.0 Depends: ggplot2, R (>= 4.3) Imports: SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang, SummarizedExperiment Suggests: STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle, ggpubr, scran, scater, scuttle, Seurat, hexbin License: MIT + file LICENSE MD5sum: 8ef194d1e67dfaa58ad286dc2978fa41 NeedsCompilation: no File: escheR_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: esetVis Version: 1.32.0 Imports: mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils, grDevices, methods Suggests: ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db License: GPL-3 MD5sum: c9143b3440c023f9ff91fe2623742f12 NeedsCompilation: no File: esetVis_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: esquisse Version: 2.1.0 Imports: bslib, datamods (>= 1.5.1), downlit, ggplot2 (>= 3.0.0), grDevices, htmltools (>= 0.5.0), jsonlite, phosphoricons (>= 0.2.1), rlang (>= 0.3.1), rstudioapi, scales, shiny (>= 1.1.0), shinybusy, shinyWidgets (>= 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KEGGREST, AnnotationDbi, GO.db Suggests: pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma License: GPL (>= 2.0) MD5sum: 2193191ffd77596b99951ed0040af87d NeedsCompilation: no File: gage_2.56.0_R_x86_64-pc-linux-gnu.tar.gz Package: gam Version: 1.22-5 Depends: R (>= 4.0), stats, splines, foreach Imports: methods Suggests: interp, testthat License: GPL-2 MD5sum: e394b9e1234824d6a06c787823a85280 NeedsCompilation: yes File: gam_1.22-5_R_x86_64-pc-linux-gnu.tar.gz Package: gamlss.data Version: 6.0-6 Depends: R (>= 3.5.0) License: GPL-2 | GPL-3 MD5sum: ab675f0a236e69e319abe9706a68f9cc NeedsCompilation: no File: gamlss.data_6.0-6_R_x86_64-pc-linux-gnu.tar.gz Package: gamlss.dist Version: 6.1-1 Depends: R (>= 3.5.0) Imports: MASS, graphics, stats, methods, grDevices Suggests: distributions3 (>= 0.2.1) License: GPL-2 | GPL-3 MD5sum: d0cc0002692b2245a51b68a2a16d8ce7 NeedsCompilation: yes File: 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ggplot2, mwcsr, pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0) Suggests: testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi, org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils License: MIT + file LICENCE MD5sum: 94519fdd3956fbb09c4bf7b632efe49c NeedsCompilation: no File: gatom_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: gbm Version: 2.2.2 Depends: R (>= 2.9.0) Imports: lattice, parallel, survival Suggests: covr, gridExtra, knitr, pdp, RUnit, splines, tinytest, vip, viridis License: GPL (>= 2) | file LICENSE MD5sum: b30735d6582b0749e5fd3ba0babca09f NeedsCompilation: yes File: gbm_2.2.2_R_x86_64-pc-linux-gnu.tar.gz Package: gbutils Version: 0.5 Depends: methods Imports: stats, utils, Rdpack (>= 0.9) Suggests: testthat (>= 3.0.0), classGraph, graph, Rgraphviz License: GPL (>= 2) MD5sum: 8a828061cd737f6796e2b296538dbaf8 NeedsCompilation: no File: gbutils_0.5_R_x86_64-pc-linux-gnu.tar.gz Package: gcapc Version: 1.30.0 Depends: R (>= 3.4) Imports: BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings, BSgenome, GenomicRanges, Rsamtools, GenomicAlignments, matrixStats, MASS, splines, grDevices, graphics, stats, methods Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 License: GPL-3 MD5sum: eb56ef485f00096fddd90f41a6c26eec NeedsCompilation: no File: gcapc_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: gcatest Version: 2.6.0 Depends: R (>= 4.0) Imports: methods, lfa Suggests: knitr, ggplot2, testthat, BEDMatrix, genio License: GPL (>= 3) MD5sum: e7b53a844043ee465dc27d77d68d6498 NeedsCompilation: no File: gcatest_2.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: gclus Version: 1.3.2 Depends: R (>= 2.10), cluster Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: a1f0ace773d9ac16be2791d2603afd98 NeedsCompilation: no File: gclus_1.3.2_R_x86_64-pc-linux-gnu.tar.gz Package: gcrma Version: 2.78.0 Depends: R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats, utils Imports: Biobase, affy (>= 1.23.2), affyio (>= 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fontquiver (>= 0.2.0), htmltools, Rcpp (>= 0.12.12), systemfonts (>= 1.1.0), tools LinkingTo: Rcpp Suggests: curl, gfonts, methods, testthat License: GPL-3 | file LICENSE MD5sum: d5d874bdeb50f04786f29400def98a5b NeedsCompilation: yes File: gdtools_0.4.1_R_x86_64-pc-linux-gnu.tar.gz Package: geNetClassifier Version: 1.46.0 Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods Imports: e1071, graphics, grDevices Suggests: leukemiasEset, RUnit, BiocGenerics Enhances: RColorBrewer, igraph, infotheo License: GPL (>= 2) MD5sum: 219c25f2f338e378f0698ff1bcfe2342 NeedsCompilation: no File: geNetClassifier_1.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: geeM Version: 0.10.1 Depends: Matrix Imports: stats, methods Suggests: geepack, testthat, MuMIn License: GPL-3 MD5sum: 09602e5d844b4223c33f83ef34d6880c NeedsCompilation: no File: geeM_0.10.1_R_x86_64-pc-linux-gnu.tar.gz Package: geepack Version: 1.3.12 Depends: R (>= 3.5.0), methods Imports: MASS, broom, magrittr License: GPL (>= 3) 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tidyr, dplyr, readr, purrr, igraph, geneplast, BiocFileCache Suggests: geneplast, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: cbf2f851b3dca50aeab54cad08a61273 NeedsCompilation: no File: geneplast.data_0.99.9_R_x86_64-pc-linux-gnu.tar.gz Package: geneplast Version: 1.32.0 Depends: R (>= 4.0), methods Imports: igraph, snow, ape, grDevices, graphics, stats, utils, data.table Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown, Fletcher2013b, geneplast.data, geneplast.data.string.v91, ggplot2, ggpubr, plyr License: GPL (>= 2) MD5sum: 72dc26c44acd7a5e196b11dbcca49f12 NeedsCompilation: no File: geneplast_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: geneplotter Version: 1.84.0 Depends: R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate Imports: AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats, utils Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db, BiocStyle, knitr License: Artistic-2.0 MD5sum: 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genomation Version: 1.38.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>= 1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute, IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix, plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern, rtracklayer (>= 1.39.7), Rcpp (>= 0.12.14) LinkingTo: Rcpp Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 28326249257a15551733351ac37be55b NeedsCompilation: yes File: genomation_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: genomeIntervals Version: 1.62.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: GenomeInfoDb (>= 1.5.8), GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 426fca019145e1603926d0073f957b07 NeedsCompilation: no File: 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graphics LinkingTo: Rcpp Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle Enhances: doMC (>= 1.3.3) License: EPL (>= 1.0) MD5sum: 5bfab2810f238319e4eb9ce435b729db NeedsCompilation: yes File: messina_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: metR Version: 0.18.0 Depends: R (>= 2.10) Imports: checkmate, data.table, digest, Formula, formula.tools, ggplot2 (>= 3.5.0), grid, gtable, memoise, plyr, scales, sf, stringr, purrr, isoband, lubridate Suggests: maps, covr, irlba, knitr, ncdf4, pkgdown, reshape2, markdown, testthat (>= 2.1.0), viridis, PCICt, gridExtra, vdiffr, proj4, kriging, terra, here, gsignal, rnaturalearth License: GPL-3 MD5sum: 49fe69d87e77d7d4403d81e3bc732241 NeedsCompilation: no File: metR_0.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: metaCCA Version: 1.34.0 Suggests: knitr License: MIT + file LICENSE MD5sum: 9dc0567ec21e4ff630a645db74d1a1c9 NeedsCompilation: no File: metaCCA_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: metaMSdata 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alabama, optimParallel, optimx, CompQuadForm, mvtnorm, BiasedUrn, Epi, survival, GLMMadaptive, glmmTMB, car, multcomp, gsl, sp, ape, boot, clubSandwich, crayon, R.rsp, testthat, rmarkdown, wildmeta, emmeans, estmeansd, metaBLUE, rstudioapi, glmulti, MuMIn, mice, Amelia, calculus License: GPL (>= 2) MD5sum: 4e89d9b1c66934e124f2b0e44709f935 NeedsCompilation: no File: metafor_4.8-0_R_x86_64-pc-linux-gnu.tar.gz Package: metagene2 Version: 1.22.0 Depends: R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel Imports: rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges, ggplot2, Rsamtools, purrr, data.table, methods, dplyr, magrittr, reshape2 Suggests: BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown License: Artistic-2.0 MD5sum: 57a1f16bd5302f4336193b8070d5f95a NeedsCompilation: no File: metagene2_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: metagenomeSeq Version: 1.48.1 Depends: R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer Imports: parallel, matrixStats, foreach, Matrix, gplots, graphics, grDevices, stats, utils, Wrench Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay, IHW License: Artistic-2.0 MD5sum: 2c6aa0f2d2f753aff045bf7a396f1722 NeedsCompilation: no File: metagenomeSeq_1.48.1_R_x86_64-pc-linux-gnu.tar.gz Package: metahdep Version: 1.64.0 Depends: R (>= 2.10), methods Suggests: affyPLM License: GPL-3 MD5sum: 9e160e3a0a21a35a8be2ec74b7ca6fbb NeedsCompilation: yes File: metahdep_1.64.0_R_x86_64-pc-linux-gnu.tar.gz Package: metap Version: 1.11 Depends: R (>= 3.5.0) Imports: lattice,Rdpack (>= 0.7),TFisher,mutoss,mathjaxr (>= 0.8-3),qqconf License: GPL-2 MD5sum: 32cf82d9f9fd90fa6837ce87dcdc1467 NeedsCompilation: no File: metap_1.11_R_x86_64-pc-linux-gnu.tar.gz Package: metapod Version: 1.14.0 Imports: Rcpp LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 838d51d3cd4789d6bf6b6a4cb2c5643a NeedsCompilation: yes File: 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knitr, RMySQL, RUnit Enhances: TCC License: GPL (>= 3) MD5sum: f2a431c65e9857bc47b82337ab08f24f NeedsCompilation: yes File: metaseqR2_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: methimpute Version: 1.28.0 Depends: R (>= 3.5.0), GenomicRanges, ggplot2 Imports: Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats, GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm, data.table LinkingTo: Rcpp Suggests: knitr, BiocStyle License: Artistic-2.0 MD5sum: 792e87f5234927f16ef932e5628b474e NeedsCompilation: yes File: methimpute_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: methodical Version: 1.2.0 Depends: GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment Imports: AnnotationHub, annotatr, BiocCheck, BiocManager, BiocParallel, BiocStyle, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, cowplot, data.table, DelayedArray, devtools, dplyr, ExperimentHub, foreach, GenomeInfoDb, HDF5Array, IRanges, knitr, MatrixGenerics, R.utils, rcmdcheck, RcppRoll, remotes, rhdf5, rtracklayer, S4Vectors, scales, tibble, tidyr, tools, TumourMethData, usethis Suggests: BSgenome.Athaliana.TAIR.TAIR9, DESeq2, methrix, rmarkdown License: GPL (>= 3) MD5sum: afbf8fd9a76d75d9086241d9fb1dc8aa NeedsCompilation: no File: methodical_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: methrix Version: 1.20.0 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment Imports: rtracklayer, DelayedArray, HDF5Array, BSgenome, DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors, matrixStats, graphics, stats, utils, GenomicRanges, IRanges Suggests: knitr, rmarkdown, DSS, bsseq, plotly, BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19, GenomicScores, Biostrings, RColorBrewer, GenomeInfoDb, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 25069e6de54438fc326ef7184160d243 NeedsCompilation: no File: methrix_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: methyLImp2 Version: 1.2.0 Depends: R (>= 4.3.0), ChAMPdata Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: 1b18356f0c0122f6549d294dbd78ccf1 NeedsCompilation: no File: methyLImp2_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylCC Version: 1.20.0 Depends: R (>= 3.6), FlowSorted.Blood.450k Imports: Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr, minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter, genefilter, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 Suggests: rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr, ggplot2 License: GPL-3 MD5sum: 7e95ed03d41db38b504f507ed0c9aa88 NeedsCompilation: no File: methylCC_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylGSA Version: 1.24.0 Depends: R (>= 3.5) Imports: RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler, missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db, AnnotationDbi, shiny, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Suggests: knitr, rmarkdown, testthat, enrichplot License: GPL-2 MD5sum: 3a1ee16b3d9d121f451fc34cca67c184 NeedsCompilation: no File: methylGSA_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylMnM Version: 1.44.0 Depends: R (>= 2.12.1), edgeR, statmod License: GPL-3 MD5sum: 791022fa72fede8ae44b4ef4d1cb0390 NeedsCompilation: yes File: methylMnM_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylPipe Version: 1.40.0 Depends: R (>= 3.5.0), methods, grDevices, graphics, stats, utils, GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools Imports: marray, gplots, IRanges, BiocGenerics, Gviz, GenomicAlignments, Biostrings, parallel, data.table, GenomeInfoDb, S4Vectors Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR License: GPL (>= 2) MD5sum: a8a272fff11d14cb4181163594113614 NeedsCompilation: yes File: methylPipe_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylSig Version: 1.18.0 Depends: R (>= 3.6) Imports: bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges, GenomeInfoDb, GenomicRanges, methods, parallel, stats, S4Vectors Suggests: BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0), covr License: GPL-3 MD5sum: db599717e9d3c90d83b80551a8c8d27e NeedsCompilation: no File: methylSig_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylclockData Version: 1.14.0 Imports: ExperimentHubData, ExperimentHub, utils Suggests: knitr, BiocStyle, rmarkdown License: MIT + file LICENSE MD5sum: f150855ce5bced820241db46952d1dae NeedsCompilation: no File: methylclockData_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylclock Version: 1.12.0 Depends: R (>= 4.1.0), methylclockData, devtools, quadprog Imports: Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute, PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2, ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra, preprocessCore, dynamicTreeCut, planet LinkingTo: Rcpp Suggests: BiocStyle, knitr, GEOquery, rmarkdown License: MIT + file LICENSE MD5sum: bede1ba5045be6606993c1981d3abe66 NeedsCompilation: yes File: methylclock_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylscaper Version: 1.14.0 Depends: R (>= 4.4.0) Imports: shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings, pwalign, Rfast, grDevices, graphics, stats, utils, tools, methods, shinyFiles, data.table, SummarizedExperiment Suggests: BiocStyle, knitr, rmarkdown, devtools, R.utils License: GPL-2 MD5sum: a2b42e9d347d2d02b56a76bd4a59a21c NeedsCompilation: no File: methylscaper_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: methylumi Version: 2.52.0 Depends: Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi Imports: BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr License: GPL-2 MD5sum: 41e5334685b2d87d803d5aede48291d2 NeedsCompilation: no File: methylumi_2.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: mfa Version: 1.28.0 Depends: R (>= 3.4.0) Imports: methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack, MCMCglmm, coda, magrittr, tibble, Biobase LinkingTo: Rcpp Suggests: knitr, rmarkdown, BiocStyle, testthat License: GPL (>= 2) MD5sum: 04630d1d74359f78b9f762aabf96cff2 NeedsCompilation: yes File: mfa_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: mgsa Version: 1.54.0 Depends: R (>= 2.14.0), methods, gplots Imports: graphics, stats, utils Suggests: DBI, RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: c14d936f3a2d0af65f36cef9b611f9f0 NeedsCompilation: yes File: mgsa_1.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: mgsub Version: 1.7.3 Suggests: covr, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: a9d479993bccce28a712c8530e27e9ef NeedsCompilation: no File: mgsub_1.7.3_R_x86_64-pc-linux-gnu.tar.gz Package: mhsmm Version: 0.4.21 Depends: mvtnorm Imports: methods License: GPL (>= 2) MD5sum: f862bd2fdc9cc2160fe63d477eacf2c6 NeedsCompilation: yes File: mhsmm_0.4.21_R_x86_64-pc-linux-gnu.tar.gz Package: miQC Version: 1.14.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: d39cb1c7448f89465eb3a9612eb104d7 NeedsCompilation: no File: miQC_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRBaseConverter Version: 1.30.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 4915d759dd5b30d5e32f313d9228bccd NeedsCompilation: no File: miRBaseConverter_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRBaseVersions.db Version: 1.1.0 Imports: AnnotationDbi, DBI, RSQLite, methods, gtools Suggests: testthat, knitr, rmarkdown, annotate License: Artistic-2.0 MD5sum: 4382d9a22631ad8a586ad498d3cb2dda NeedsCompilation: no File: miRBaseVersions.db_1.1.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRLAB Version: 1.36.0 Imports: methods, stats, utils, RCurl, httr, stringr, Hmisc, energy, entropy, gplots, glmnet, impute, limma, pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc, InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit,rmarkdown License: GPL (>= 2) MD5sum: 2197b5c0febdd28d2d4b6f28c83a6f81 NeedsCompilation: no File: miRLAB_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRNATarget Version: 1.44.0 Depends: R (>= 2.10), Biobase License: GPL MD5sum: fa51e85103e1b176ddfeb7dd918d9ae3 NeedsCompilation: no File: miRNATarget_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRNAmeConverter Version: 1.34.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 98b587527dc0c04cbdb40bf702e52cb9 NeedsCompilation: no File: miRNAmeConverter_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRNApath Version: 1.66.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 8417d7e5c9829d920d537580192f29cd NeedsCompilation: no File: miRNApath_1.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRNAtap.db Version: 0.99.10 Depends: miRNAtap Imports: AnnotationDbi, DBI, RSQLite, miRNAtap License: GPL-2 MD5sum: 5831a7a6ff4bb894f76b79db466ecdf3 NeedsCompilation: no File: miRNAtap.db_0.99.10_R_x86_64-pc-linux-gnu.tar.gz Package: miRNAtap Version: 1.40.0 Depends: R (>= 3.3.0), AnnotationDbi Imports: DBI, RSQLite, stringr, sqldf, plyr, methods Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat License: GPL-2 MD5sum: f03c4b84f25aa63dae8554c1cad95fb3 NeedsCompilation: no File: miRNAtap_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRSM Version: 2.2.0 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE, MatrixCorrelation, energy Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 49f53dc0ee6842ae4c4ffad94cda1421 NeedsCompilation: yes File: miRSM_2.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRcompData Version: 1.36.0 Depends: R (>= 3.2), Imports: utils License: GPL-3 | file LICENSE MD5sum: d2774994e09f27d5ca4b2504c68dc60f NeedsCompilation: no File: miRcompData_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRcomp Version: 1.36.0 Depends: R (>= 3.2), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 68e86d3530d035269d540ef5eb2374b8 NeedsCompilation: no File: miRcomp_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: miRspongeR Version: 2.10.0 Depends: R (>= 4.4.0) Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler, ReactomePA, DOSE, survival, grDevices, graphics, stats, linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL-3 MD5sum: 495b5e0520a1717ed56446dc47a8e41b NeedsCompilation: yes File: miRspongeR_2.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: miaSim Version: 1.12.0 Depends: TreeSummarizedExperiment Imports: SummarizedExperiment, deSolve, stats, poweRlaw, MatrixGenerics, S4Vectors Suggests: ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2, igraph, network, reshape2, sna, vegan, rmarkdown, knitr, BiocStyle, testthat, mia, miaViz, colourvalues, philentropy License: Artistic-2.0 | file LICENSE MD5sum: 2c512cb7419eef4238c94039bbcc2c9c NeedsCompilation: no File: miaSim_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: miaViz Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia (>= 1.13.0), ggplot2, ggraph (>= 2.0) Imports: methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytext, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, bluster, ComplexHeatmap, circlize License: Artistic-2.0 | file LICENSE MD5sum: 8099af14d3dc5dedba9d37679bfb7325 NeedsCompilation: no File: miaViz_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: mia Version: 1.14.0 Depends: R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan Suggests: ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: 8390e2a3293f1f0cf1aa1a91e51abfdb NeedsCompilation: no File: mia_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: mice Version: 3.17.0 Depends: R (>= 2.10.0) Imports: broom, dplyr, glmnet, graphics, grDevices, lattice, mitml, nnet, Rcpp, rpart, stats, tidyr, utils LinkingTo: cpp11, Rcpp Suggests: broom.mixed, future, furrr, haven, knitr, literanger, lme4, MASS, miceadds, pan, parallelly, purrr, ranger, randomForest, rmarkdown, rstan, survival, testthat License: GPL (>= 2) MD5sum: 4561b439ae17e5e2d94a6c9d32188ecd NeedsCompilation: yes File: mice_3.17.0_R_x86_64-pc-linux-gnu.tar.gz Package: microSTASIS Version: 1.6.0 Depends: R (>= 4.2.0) Imports: BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr, TreeSummarizedExperiment Suggests: BiocStyle, gghighlight, knitr, rmarkdown, methods, RefManageR, sessioninfo, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: GPL-3 MD5sum: 62bd562caa289c7d0070ba14711ecbe8 NeedsCompilation: no File: microSTASIS_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: microbenchmark Version: 1.5.0 Depends: R (>= 3.2.0) Imports: graphics, stats Suggests: ggplot2, multcomp, RUnit License: BSD_2_clause + file LICENSE MD5sum: 60c832968a5d5c9e634a6f30c567faa9 NeedsCompilation: yes File: microbenchmark_1.5.0_R_x86_64-pc-linux-gnu.tar.gz Package: microbiomeDASim Version: 1.20.0 Depends: R (>= 3.6.0) Imports: graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase Suggests: testthat (>= 2.1.0), knitr, devtools License: MIT + file LICENSE MD5sum: 1af859d622fe6ef1ae1e18c88cabe7c5 NeedsCompilation: no File: microbiomeDASim_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: microbiomeDataSets Version: 1.14.0 Depends: R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment, MultiAssayExperiment Imports: methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat License: CC0 MD5sum: c2db19ccc4fb84ef5753c9a039d0fd91 NeedsCompilation: no File: microbiomeDataSets_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: microbiomeExplorer Version: 1.16.0 Depends: shiny, magrittr, metagenomeSeq, Biobase Imports: shinyjs (>= 2.0.0), shinydashboard, shinycssloaders, shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr, purrr, rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools, stringr, vegan, matrixStats, heatmaply, car, broom, limma, reshape2, tibble, forcats, lubridate, methods, plotly (>= 4.9.1) Suggests: V8, testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: 4db6b236a65bb4cd38b059f50abd2a5d NeedsCompilation: no File: microbiomeExplorer_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: microbiomeMarker Version: 1.12.2 Depends: R (>= 4.1.0) Imports: dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2, tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges, tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR, BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase, ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest, plotROC, vegan, pROC, BiocParallel Suggests: testthat, covr, glmnet, Matrix, kernlab, e1071, ranger, knitr, rmarkdown, BiocStyle, withr, microbiome License: GPL-3 MD5sum: 3d598e9b0d936beb3f26ff5fa98ad8bf NeedsCompilation: no File: microbiomeMarker_1.12.2_R_x86_64-pc-linux-gnu.tar.gz Package: microbiome Version: 1.28.0 Depends: R (>= 3.6.0), phyloseq, ggplot2 Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat License: BSD_2_clause + file LICENSE MD5sum: d316cc2e9f508f99635844e7192bb306 NeedsCompilation: no File: microbiome_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: midasHLA Version: 1.14.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 1.8.3) Imports: assertthat (>= 0.2.0), broom (>= 0.5.1), dplyr (>= 0.8.0.1), formattable (>= 0.2.0.1), HardyWeinberg (>= 1.6.3), kableExtra (>= 1.1.0), knitr (>= 1.21), magrittr (>= 1.5), methods, stringi (>= 1.2.4), rlang (>= 0.3.1), S4Vectors (>= 0.20.1), stats, SummarizedExperiment (>= 1.12.0), tibble (>= 2.0.1), utils, qdapTools (>= 1.3.3) Suggests: broom.mixed (>= 0.2.4), cowplot (>= 1.0.0), devtools (>= 2.0.1), ggplot2 (>= 3.1.0), ggpubr (>= 0.2.5), rmarkdown, seqinr (>= 3.4-5), survival (>= 2.43-3), testthat (>= 2.0.1), tidyr (>= 1.1.2) License: MIT + file LICENCE MD5sum: 323d1a08733b4d98c4d4e19ccd25bd35 NeedsCompilation: no File: midasHLA_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: miloR Version: 2.2.0 Depends: R (>= 4.0.0), edgeR Imports: BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>= 1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods, igraph, irlba, utils, cowplot, BiocParallel, BiocSingular, limma, ggplot2, tibble, matrixStats, ggraph, gtools, SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppML Suggests: testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown, uwot, scuttle, BiocStyle, MouseGastrulationData, MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq, graphics, sparseMatrixStats License: GPL-3 + file LICENSE MD5sum: 8eed02e0c36d7aa0a00bca1ccd0cf59f NeedsCompilation: yes File: miloR_2.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: mina Version: 1.14.0 Depends: R (>= 4.0.0) Imports: methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory, foreach, ggplot2, parallel, parallelDist, reshape2, plyr, biganalytics, stringr, Hmisc, utils LinkingTo: Rcpp, RcppParallel, RcppArmadillo Suggests: knitr, rmarkdown Enhances: doMC License: GPL MD5sum: 95e4d66831d583719c0f2960d8d876f9 NeedsCompilation: yes File: mina_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: minet Version: 3.64.0 Imports: infotheo License: Artistic-2.0 MD5sum: 85e9bb205bcb1e61ee5b814a823bdded NeedsCompilation: yes File: minet_3.64.0_R_x86_64-pc-linux-gnu.tar.gz Package: minfiDataEPIC Version: 1.32.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19 License: Artistic-2.0 MD5sum: f12b35e42bc8e20b1b68108e8868dc46 NeedsCompilation: no File: minfiDataEPIC_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: minfiData Version: 0.52.0 Depends: R (>= 3.5.0), minfi (>= 1.21.2), IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19 License: Artistic-2.0 MD5sum: 416788618459a6c31d90421d67008735 NeedsCompilation: no File: minfiData_0.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: minfi Version: 1.52.1 Depends: methods, BiocGenerics (>= 0.15.3), GenomicRanges, SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>= 1.1.9) Imports: S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges, beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma, preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>= 1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog, data.table, GEOquery, stats, grDevices, graphics, utils, DelayedArray (>= 0.15.16), HDF5Array, BiocParallel Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools License: Artistic-2.0 MD5sum: cf6f53c4f436731734179daffaf21675 NeedsCompilation: no File: minfi_1.52.1_R_x86_64-pc-linux-gnu.tar.gz Package: minionSummaryData Version: 1.36.0 Depends: R (>= 3.2.0) Suggests: BiocStyle, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 07e37d8e9be06ed22dabe3bdc6e9cfaa NeedsCompilation: no 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BiocGenerics, GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylationEPICv2manifest, IRanges, limma, methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod, stringr, SummarizedExperiment Suggests: BiocStyle, edgeR, knitr, minfiData, rmarkdown, tweeDEseqCountData, DMRcate, ExperimentHub License: GPL-2 MD5sum: 64030a189ca1a3fd36dab86f946e25ab NeedsCompilation: no File: missMethyl_1.40.3_R_x86_64-pc-linux-gnu.tar.gz Package: missRows Version: 1.26.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 4041fd3df30ce8c1aad0b8359bb3a2d6 NeedsCompilation: no File: missRows_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: mistyR Version: 1.14.0 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, 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mice, miceadds, Amelia, lme4, nlme, lavaan, geepack, glmmTMB, survival, knitr, rmarkdown License: GPL (>= 2) MD5sum: bea3d406abb6e062d872a4f64e22aa26 NeedsCompilation: no File: mitml_0.4-5_R_x86_64-pc-linux-gnu.tar.gz Package: mitoClone2 Version: 1.12.0 Depends: R (>= 4.1.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 0937704a56b5ff97bbb55096dcf6da1a NeedsCompilation: yes File: mitoClone2_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: mitools Version: 2.4 Imports: DBI, methods, stats Suggests: RODBC, foreign License: GPL-2 MD5sum: d19be134da0bebc8dab8408998b37c58 NeedsCompilation: no File: mitools_2.4_R_x86_64-pc-linux-gnu.tar.gz Package: mixOmics Version: 6.30.0 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, 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Imports: cluster, graph, Rgraphviz, flexclust, lattice, naturalsort, snowfall, stats4, tsne, methods, graphics, stats, utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices, e1071, ggplot2, wesanderson LinkingTo: Rcpp, RcppEigen Suggests: knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM, BiocStyle License: GPL-3 MD5sum: a6868d6c6a2eb74a86f05873bce9f54b NeedsCompilation: yes File: mnem_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: mnormt Version: 2.1.1 Depends: R (>= 2.2.0) License: GPL-2 | GPL-3 MD5sum: 3beedfe12f76f33727110af67ea41637 NeedsCompilation: yes File: mnormt_2.1.1_R_x86_64-pc-linux-gnu.tar.gz Package: moanin Version: 1.14.0 Depends: R (>= 4.0), SummarizedExperiment, topGO, stats Imports: S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics, methods, grDevices, reshape2, NMI, zoo, ClusterR, splines, matrixStats Suggests: testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown, markdown, covr, BiocStyle License: BSD 3-clause License + file LICENSE MD5sum: 246cc618fc831f9923774cad525d8dba NeedsCompilation: no File: moanin_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: mobileRNA Version: 1.2.0 Depends: R (>= 4.3.0) Imports: dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel, grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer, GenomicRanges, rtracklayer, data.table, SimDesign, scales, IRanges, stats, methods, Biostrings, reticulate, S4Vectors, GenomeInfoDb, SummarizedExperiment, rlang, bioseq, grid Suggests: knitr, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: ca2769c50c1005e5e99125eabb86c1c5 NeedsCompilation: no File: mobileRNA_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: mockery Version: 0.4.4 Imports: testthat Suggests: knitr, R6, rmarkdown (>= 1.0) License: MIT + file LICENSE MD5sum: 1e758c15dc7726c188791c994b3c0cdb NeedsCompilation: no File: mockery_0.4.4_R_x86_64-pc-linux-gnu.tar.gz Package: mockr Version: 0.2.1 Imports: rlang, withr Suggests: covr, fs, knitr, pkgload, rmarkdown, testthat, usethis License: GPL-3 MD5sum: 539ceca7c5c6b46dbd372c5fffd37c82 NeedsCompilation: no File: mockr_0.2.1_R_x86_64-pc-linux-gnu.tar.gz Package: modeest Version: 2.4.0 Depends: R (>= 3.2) Imports: fBasics, stable, stabledist, stats, statip (>= 0.2.3) Suggests: evd, knitr, mvtnorm, testthat, VGAM License: GPL-3 MD5sum: c6ebcfcfa5cb79d7f64edc6dd9060756 NeedsCompilation: no File: modeest_2.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: modelr Version: 0.1.11 Depends: R (>= 3.2) Imports: broom, magrittr, purrr (>= 0.2.2), rlang (>= 1.0.6), tibble, tidyr (>= 0.8.0), tidyselect, vctrs Suggests: compiler, covr, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 87b74132a92aacbf132fa7dfbd03ed8e NeedsCompilation: no File: modelr_0.1.11_R_x86_64-pc-linux-gnu.tar.gz Package: modeltools Version: 0.2-23 Depends: stats, stats4 Imports: methods License: GPL-2 MD5sum: 7d28fdbdb8365a239403019585a65aaa NeedsCompilation: no File: modeltools_0.2-23_R_x86_64-pc-linux-gnu.tar.gz Package: mogsa Version: 1.40.0 Depends: R (>= 3.4.0) Imports: methods, graphite, genefilter, BiocGenerics, gplots, GSEABase, Biobase, parallel, corpcor, svd, cluster, grDevices, graphics, stats, utils Suggests: BiocStyle, knitr, org.Hs.eg.db License: GPL-2 MD5sum: 7c39c4e55e315ae533395126507c7759 NeedsCompilation: no File: mogsa_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: moments Version: 0.14.1 License: GPL (>= 2) MD5sum: 474072d7f041704fb679f45a889e0d1a NeedsCompilation: no File: moments_0.14.1_R_x86_64-pc-linux-gnu.tar.gz Package: monaLisa Version: 1.12.0 Depends: R (>= 4.1) Imports: methods, stats, utils, grDevices, graphics, BiocGenerics, GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome, glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid, circlize, ComplexHeatmap (>= 2.11.1), XVector, GenomeInfoDb, tools, vioplot, RSQLite Suggests: JASPAR2020, JASPAR2024, BSgenome.Mmusculus.UCSC.mm10, TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat, BiocStyle, gridExtra License: GPL (>= 3) MD5sum: 6f2f8686e0aa63ebe8eab47469abad43 NeedsCompilation: no File: monaLisa_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: monocle Version: 2.34.0 Depends: R (>= 2.10.0), methods, Matrix (>= 1.2-6), Biobase, ggplot2 (>= 1.0.0), VGAM (>= 1.0-6), DDRTree (>= 0.1.4), Imports: parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>= 0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>= 2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>= 0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0) LinkingTo: Rcpp Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat License: Artistic-2.0 MD5sum: ae676e9912dbecb00f51e3f8fca18e2e NeedsCompilation: yes File: monocle_2.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: mosaicCore Version: 0.9.4.0 Depends: R (>= 4.1.0) Imports: stats, dplyr, rlang, tidyr, MASS Suggests: mosaicData, mosaic, ggformula, NHANES, testthat, mosaicCalc (>= 0.5.9) License: GPL (>= 2) MD5sum: 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LICENSE MD5sum: f5722685be4f7c346cc7756432150002 NeedsCompilation: yes File: mosbi_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: mosdef Version: 1.2.0 Depends: R (>= 4.4.0) Imports: DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools, methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq, utils, RColorBrewer, rlang, DESeq2, scales, SummarizedExperiment, S4Vectors, stats Suggests: knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic, testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene, BiocStyle License: MIT + file LICENSE MD5sum: a02f7a71e7d53fff78b96b81ba5c4fbc NeedsCompilation: no File: mosdef_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: motifStack Version: 1.50.0 Depends: R (>= 2.15.1), methods, grid Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020 License: GPL (>= 2) MD5sum: 813b19f8ab65524ea803fc64663908be NeedsCompilation: no File: motifStack_1.50.0_R_x86_64-pc-linux-gnu.tar.gz Package: motifTestR Version: 1.2.1 Depends: Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0), Imports: GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer, testthat (>= 3.0.0) License: GPL-3 MD5sum: 22c980395b96f277a5e98dd1f17f0514 NeedsCompilation: no File: motifTestR_1.2.1_R_x86_64-pc-linux-gnu.tar.gz Package: motifbreakR Version: 2.20.0 Depends: R (>= 4.4.0), grid, MotifDb Imports: methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment, pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38 License: GPL-2 MD5sum: 96c5e71017dd0586e1df78165f45034c NeedsCompilation: no File: motifbreakR_2.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: motifcounter Version: 1.30.0 Depends: R(>= 3.0) Imports: Biostrings, methods Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc License: GPL-2 MD5sum: 6cfe7b386ff05ac5fbd96f45f2614499 NeedsCompilation: yes File: motifcounter_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: motifmatchr Version: 1.28.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, GenomeInfoDb LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: d7a6699f5e14db61f33a7eb6a7a6941c NeedsCompilation: yes File: motifmatchr_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: mouse4302.db Version: 3.13.0 Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.53.2), org.Mm.eg.db (>= 3.13.0) Imports: methods, AnnotationDbi Suggests: DBI, annotate, RUnit License: Artistic-2.0 MD5sum: c93d10d5833bca54f191ec2052720971 NeedsCompilation: no File: mouse4302.db_3.13.0_R_x86_64-pc-linux-gnu.tar.gz Package: mouse4302cdf Version: 2.18.0 Depends: utils Imports: AnnotationDbi License: LGPL MD5sum: 75be91294bc143e9e600365dab893f46 NeedsCompilation: no File: mouse4302cdf_2.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: mouse4302frmavecs Version: 1.5.0 Depends: R (>= 2.10.0) License: GPL (>= 2) MD5sum: ed8d20f5c855892bac426d3756d13e65 NeedsCompilation: no File: mouse4302frmavecs_1.5.0_R_x86_64-pc-linux-gnu.tar.gz Package: mpm Version: 1.0-23 Depends: R (>= 2.10) Imports: MASS, KernSmooth License: GPL (>= 2) MD5sum: 7166c82f11bf35a0e56842561f0dd764 NeedsCompilation: no File: mpm_1.0-23_R_x86_64-pc-linux-gnu.tar.gz Package: mpra Version: 1.28.0 Depends: R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, limma Imports: S4Vectors, scales, stats, graphics, statmod Suggests: BiocStyle, knitr, rmarkdown, RUnit License: Artistic-2.0 MD5sum: 1aa5a28284aca42e261bbb40f93da626 NeedsCompilation: no File: mpra_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: mrfDepth Version: 1.0.17 Depends: R (>= 3.6.0), ggplot2 Imports: abind, geometry, grid, matrixStats, reshape2, Rcpp (>= 0.12.6) LinkingTo: RcppEigen (>= 0.3.2.9.0), Rcpp (>= 0.12.6), RcppArmadillo (>= 0.7.600.1.0) Suggests: robustbase License: GPL (>= 2) MD5sum: 0568cc8a8212714aaa48bdb1032e27ee NeedsCompilation: yes File: mrfDepth_1.0.17_R_x86_64-pc-linux-gnu.tar.gz Package: msImpute Version: 1.16.0 Depends: R (>= 3.5.0) Imports: softImpute, methods, stats, graphics, pdist, reticulate, scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr, dplyr Suggests: BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD License: GPL (>= 2) MD5sum: 66127c125670f76af98023f96843a286 NeedsCompilation: no File: msImpute_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: msPurityData Version: 1.34.0 Suggests: knitr License: GPL (>= 2) MD5sum: bc49bbb005d3a23846071cea21c513a6 NeedsCompilation: no File: msPurityData_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: msPurity Version: 1.32.0 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: d279c77d92e7783f7e76a21deaa7a074 NeedsCompilation: no File: msPurity_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: msa Version: 1.38.0 Depends: R (>= 3.3.0), methods, Biostrings (>= 2.40.0) Imports: Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0), S4Vectors, tools LinkingTo: Rcpp Suggests: Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign License: GPL (>= 2) MD5sum: 14aa921c8db0b39e3ff9311db54d78c8 NeedsCompilation: yes File: msa_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: msd16s Version: 1.26.0 Depends: R (>= 2.10), Biobase, metagenomeSeq, License: Artistic-2.0 MD5sum: a89a24db6bfb45221b4bf6a951bf5289 NeedsCompilation: no File: msd16s_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: msdata Version: 0.46.0 Depends: R (>= 3.5.0) Suggests: xcms, mzR, MSnbase License: GPL (>= 2) MD5sum: eed0321f014f76a3cafc7a9bdc8eb0c0 NeedsCompilation: no File: msdata_0.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: msentropy Version: 0.1.4 Depends: R (>= 3.5.0), Rcpp (>= 1.0.10) LinkingTo: Rcpp Suggests: testthat License: Apache License (== 2.0) MD5sum: 54c1b715759e99915c5caa866e3ad261 NeedsCompilation: yes File: msentropy_0.1.4_R_x86_64-pc-linux-gnu.tar.gz Package: msgbsR Version: 1.30.0 Depends: R (>= 3.5.0), GenomicRanges, methods Imports: BSgenome, easyRNASeq, edgeR, GenomicAlignments, GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges, parallel, plyr, Rsamtools, R.utils, stats, SummarizedExperiment, S4Vectors, utils Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-2 MD5sum: d7cb3ece101524806fc32ac9a48bc5b9 NeedsCompilation: no File: msgbsR_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: msgps Version: 1.3.5 License: GPL (>= 2) MD5sum: bdb89c6fdb975ad581231bf26b51f23a NeedsCompilation: yes File: msgps_1.3.5_R_x86_64-pc-linux-gnu.tar.gz Package: msigdb Version: 1.14.0 Depends: R (>= 4.1) Imports: ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db, AnnotationDbi, methods, stats, AnnotationHub Suggests: singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown, testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma License: CC BY 4.0 MD5sum: 746a9dcdb3073e851ac350be3327fbf7 NeedsCompilation: no File: msigdb_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: msigdbr Version: 7.5.1 Depends: R (>= 3.4) Imports: babelgene, dplyr (>= 0.7.0), magrittr, rlang, tibble, tidyselect Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 37da8c11b7fb5fd14cf99ec12f1094d0 NeedsCompilation: no File: msigdbr_7.5.1_R_x86_64-pc-linux-gnu.tar.gz Package: mslp Version: 1.8.0 Depends: R (>= 4.2.0) Imports: data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils Suggests: BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest License: GPL-3 MD5sum: 4549164ce61728c627e764ab7750bafa NeedsCompilation: no File: mslp_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: msm Version: 1.8.2 Imports: survival, mvtnorm, expm, generics, tibble Suggests: mstate, minqa, doParallel, foreach, numDeriv, testthat, flexsurv, covr License: GPL (>= 2) MD5sum: 0a8dabce0bdfaba53ae4a6192d6d1083 NeedsCompilation: yes File: msm_1.8.2_R_x86_64-pc-linux-gnu.tar.gz Package: msmsEDA Version: 1.44.0 Depends: R (>= 3.0.1), MSnbase Imports: MASS, gplots, RColorBrewer License: GPL-2 MD5sum: 0daf7e38e9aaa2990a903751052d92b1 NeedsCompilation: no File: msmsEDA_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: msmsTests Version: 1.44.0 Depends: R (>= 3.0.1), MSnbase, msmsEDA Imports: edgeR, qvalue Suggests: xtable License: GPL-2 MD5sum: 317ad8ec3e6224aac8f30b5ddf113ce7 NeedsCompilation: no File: msmsTests_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: msqrob2 Version: 1.14.1 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools Suggests: multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata, MSnbase, matrixStats, MsCoreUtils, covr License: Artistic-2.0 MD5sum: 271c4e43593016e65c90f0b305447794 NeedsCompilation: no File: msqrob2_1.14.1_R_x86_64-pc-linux-gnu.tar.gz Package: mstate Version: 0.3.3 Depends: survival (>= 3.1) Imports: rlang, data.table, lattice, RColorBrewer, viridisLite Suggests: cmprsk, ggplot2, knitr, rmarkdown, relsurv (>= 2.2-5) License: GPL (>= 2) MD5sum: 799a55577cee5a107fc587bda51e4fae NeedsCompilation: yes File: mstate_0.3.3_R_x86_64-pc-linux-gnu.tar.gz Package: mtbls2 Version: 1.36.0 Depends: R (>= 2.10) Suggests: xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp, rmarkdown License: CC0 MD5sum: 71182a748ca3c146adb0507fdb14d908 NeedsCompilation: no File: mtbls2_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: multcompView Version: 0.1-10 Imports: grid Suggests: multcomp, pgirmess, MASS License: GPL MD5sum: d383ae7653b2cbea96e7c0da797ca81b NeedsCompilation: no File: multcompView_0.1-10_R_x86_64-pc-linux-gnu.tar.gz Package: multcomp Version: 1.4-28 Depends: stats, graphics, mvtnorm (>= 1.0-10), survival (>= 2.39-4), TH.data (>= 1.0-2) Imports: sandwich (>= 2.3-0), codetools Suggests: lme4 (>= 0.999375-16), nlme, robustbase, coin, MASS, foreign, xtable, lmtest, coxme (>= 2.2-1), SimComp, ISwR, tram (>= 0.2-5), fixest (>= 0.10), glmmTMB, DoseFinding, HH, asd, gsDesign, lattice License: GPL-2 MD5sum: aee929a73e831097618f1ab0184bf62e NeedsCompilation: no File: multcomp_1.4-28_R_x86_64-pc-linux-gnu.tar.gz Package: multiClust Version: 1.36.0 Imports: mclust, ctc, survival, cluster, dendextend, amap, graphics, grDevices Suggests: knitr, rmarkdown, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery License: GPL (>= 2) MD5sum: 1e192a279bf4cb8067c444f6c1257da6 NeedsCompilation: no File: multiClust_1.36.0_R_x86_64-pc-linux-gnu.tar.gz Package: multiGSEA Version: 1.16.2 Depends: R (>= 4.0.0) Imports: magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr, fgsea, metap, rappdirs, rlang, methods Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0) License: GPL-3 MD5sum: ece0487d79b8657e94f06a18b18a305f NeedsCompilation: no File: multiGSEA_1.16.2_R_x86_64-pc-linux-gnu.tar.gz Package: multiHiCcompare Version: 1.24.0 Depends: R (>= 4.0.0) Imports: data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation Suggests: knitr, rmarkdown, testthat, BiocStyle License: MIT + file LICENSE MD5sum: be91eb6bc64d86e59fbc80d809274bf1 NeedsCompilation: no File: multiHiCcompare_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: multiMiR Version: 1.28.0 Depends: R (>= 3.4) Imports: stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods, BiocGenerics, AnnotationDbi, dplyr, Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) License: MIT + file LICENSE MD5sum: d00f57f24aed7655c8cf851f6b7dccc3 NeedsCompilation: no File: multiMiR_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: multiWGCNA Version: 1.4.0 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 236b58a120156b7c61bb5bc4e6b48d4c NeedsCompilation: no File: multiWGCNA_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: multicool Version: 1.0.1 Depends: methods, Rcpp (>= 0.11.2) LinkingTo: Rcpp License: GPL-2 MD5sum: f8e008bc0d8ef3419d3bd7a323d468b3 NeedsCompilation: yes File: multicool_1.0.1_R_x86_64-pc-linux-gnu.tar.gz Package: multicrispr Version: 1.16.1 Depends: R (>= 4.0) Imports: BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, grid, karyoploteR, magrittr, methods, parallel, plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi, tidyr, tidyselect, utils Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr, magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL-2 MD5sum: 12103fd113b6191dd3a6846f378db583 NeedsCompilation: no File: multicrispr_1.16.1_R_x86_64-pc-linux-gnu.tar.gz Package: multiscan Version: 1.66.0 Depends: R (>= 2.3.0) Imports: Biobase, utils License: GPL (>= 2) MD5sum: d5437a02ed0119023b79bcf4e34352b4 NeedsCompilation: yes File: multiscan_1.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: multistateQTL Version: 1.2.2 Depends: QTLExperiment, SummarizedExperiment, ComplexHeatmap, data.table, collapse Imports: methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices Suggests: testthat, BiocStyle, knitr, covr, rmarkdown License: GPL-3 MD5sum: 027368a4637625c51a3443fcfb5b8a14 NeedsCompilation: no File: multistateQTL_1.2.2_R_x86_64-pc-linux-gnu.tar.gz Package: multitaper Version: 1.0-17 Depends: R (>= 3.0), methods Suggests: psd, fftwtools, slp License: GPL (>= 2) MD5sum: 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file LICENSE MD5sum: f554015b6fc798120aaa7ed790f6ade6 NeedsCompilation: no File: munsell_0.5.1_R_x86_64-pc-linux-gnu.tar.gz Package: muscData Version: 1.20.0 Depends: R (>= 3.6), ExperimentHub, SingleCellExperiment Imports: utils Suggests: BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix, matrixStats, methods, muscat, rmarkdown, R.utils, readxl, scater, scds, Seurat License: MIT + file LICENSE MD5sum: 39d341e66b3219180be921695d23322c NeedsCompilation: no File: muscData_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: muscat Version: 1.20.0 Depends: R (>= 4.4) Imports: BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr, edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest, lme4, Matrix, matrixStats, methods, progress, purrr, rlang, S4Vectors, scales, scater, scuttle, sctransform, stats, SingleCellExperiment, SummarizedExperiment, variancePartition, viridis Suggests: BiocStyle, countsimQC, ExperimentHub, iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2, rmarkdown, statmod, stageR, testthat, UpSetR License: GPL-3 MD5sum: 98540fbae95942d006b2f56e86e63419 NeedsCompilation: no File: muscat_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: musicatk Version: 2.0.0 Depends: R (>= 4.4.0), NMF Imports: SummarizedExperiment, VariantAnnotation, Biostrings, base, methods, magrittr, tibble, tidyr, gtools, gridExtra, MCMCprecision, MASS, matrixTests, data.table, dplyr, rlang, BSgenome, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, S4Vectors, uwot, ggplot2, stringr, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10, decompTumor2Sig, topicmodels, ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap, philentropy, maftools, shiny, stringi, tidyverse, ggpubr, Matrix (>= 1.6.1), scales, conclust Suggests: TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard, shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr, rmarkdown, survival, XVector, qpdf, covr, shinyWidgets, cowplot, withr License: LGPL-3 MD5sum: 08478e8183d98093e0af8b02d99927e2 NeedsCompilation: no File: musicatk_2.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: mutoss Version: 0.1-13 Depends: R (>= 2.10.0), mvtnorm Imports: plotrix, multtest (>= 2.2.0), multcomp (>= 1.1-0), methods Suggests: fdrtool, qvalue, testthat, lattice License: GPL MD5sum: 16263007388361cc78ab9fa574501196 NeedsCompilation: no File: mutoss_0.1-13_R_x86_64-pc-linux-gnu.tar.gz Package: mvnfast Version: 0.2.8 Imports: Rcpp LinkingTo: Rcpp, RcppArmadillo, BH Suggests: knitr, rmarkdown, testthat, mvtnorm, microbenchmark, MASS, plyr, RhpcBLASctl License: GPL (>= 2.0) MD5sum: 6c87170f3fff8d76d3faa3bebad9f38f NeedsCompilation: yes File: mvnfast_0.2.8_R_x86_64-pc-linux-gnu.tar.gz Package: mvoutData Version: 1.42.0 Depends: R (>= 2.10.0), methods, Biobase (>= 2.5.5), affy (>= 1.23.4), lumi License: Artistic-2.0 MD5sum: f7ae2c6845fdbbbbbc7c28859a2d4e57 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xml2, utils, methods, grDevices, ggplot2, IRanges, GenomicRanges, S4Vectors Suggests: knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics License: GPL-3 MD5sum: a344580dfcb462f675f544124aa20055 NeedsCompilation: no File: ncRNAtools_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: ncdf4 Version: 1.23 License: GPL (>= 3) MD5sum: c32021fe534b0f07b10be32d865362f6 NeedsCompilation: yes File: ncdf4_1.23_R_x86_64-pc-linux-gnu.tar.gz Package: ncdfFlow Version: 2.52.1 Depends: R (>= 2.14.0), flowCore(>= 1.51.7), methods, BH Imports: Biobase,BiocGenerics,flowCore LinkingTo: cpp11,BH, Rhdf5lib Suggests: testthat,parallel,flowStats,knitr MD5sum: 844bf6ed6b6ca2fbd256bcdd03d34fb8 NeedsCompilation: yes File: ncdfFlow_2.52.1_R_x86_64-pc-linux-gnu.tar.gz Package: ndexr Version: 1.28.0 Depends: RCX Imports: httr, jsonlite, plyr, tidyr Suggests: BiocStyle, testthat, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 0d8d0e6965c0afc5b66edfd7e2369083 NeedsCompilation: no File: 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TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata, txdbmaker License: MIT + file LICENSE MD5sum: 71946ee51ed72635adcd877cfe735f5b NeedsCompilation: yes File: raer_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: raerdata Version: 1.4.0 Imports: ExperimentHub, Rsamtools, BiocGenerics, rtracklayer, SingleCellExperiment Suggests: rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8e65749e077a9139672e41fb1b2226a0 NeedsCompilation: no File: raerdata_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: rafalib Version: 1.0.0 Imports: RColorBrewer License: Artistic-2.0 MD5sum: c51850caff3129054c5b062590b0bd33 NeedsCompilation: no File: rafalib_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: rain Version: 1.40.0 Depends: R (>= 2.10), gmp, multtest Suggests: lattice, BiocStyle License: GPL-2 MD5sum: b226e56db029fe7678c8dfcbc680e817 NeedsCompilation: no File: 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pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 License: LGPL-3 MD5sum: 94459a74c5445e50c0728264ede58023 NeedsCompilation: yes File: ramwas_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: randPack Version: 1.52.0 Depends: methods Imports: Biobase License: Artistic-2.0 MD5sum: 44c299afc18ce9c769be8012612cd0e9 NeedsCompilation: no File: randPack_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: randRotation Version: 1.18.0 Imports: methods, graphics, utils, stats, Rdpack (>= 0.7) Suggests: knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle, testthat (>= 2.1.0), limma, sva License: GPL-3 MD5sum: 9ec83b690188145622839f29436589ba NeedsCompilation: no File: randRotation_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: randomForestSRC Version: 3.3.3 Depends: R (>= 4.3.0), Imports: parallel, data.tree, DiagrammeR Suggests: survival, pec, prodlim, mlbench, interp, caret, imbalance, cluster, fst, data.table License: GPL (>= 3) MD5sum: 7c5e0fbc485f83819b46e6841554988d NeedsCompilation: yes File: 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LICENSE MD5sum: 0f9c5b6e78f7728866a64a3f66a7f249 NeedsCompilation: no File: rematch_2.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: rentrez Version: 1.2.3 Depends: R (>= 2.6.0) Imports: XML, httr (>= 0.5), jsonlite (>= 0.9) Suggests: testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 5ca18b0750bc7a2cb842345b03245ecc NeedsCompilation: no File: rentrez_1.2.3_R_x86_64-pc-linux-gnu.tar.gz Package: renv Version: 1.1.2 Imports: utils Suggests: BiocManager, cli, compiler, covr, cpp11, devtools, gitcreds, jsonlite, jsonvalidate, knitr, miniUI, modules, packrat, pak, R6, remotes, reticulate, rmarkdown, rstudioapi, shiny, testthat, uuid, waldo, yaml, webfakes License: MIT + file LICENSE MD5sum: f5fcfe76d71a92de57b3a656cd79a28b NeedsCompilation: no File: renv_1.1.2_R_x86_64-pc-linux-gnu.tar.gz Package: repmis Version: 0.5 Depends: R (>= 3.0.0) Imports: data.table, digest, httr, plyr, R.cache Suggests: xlsx License: GPL (>= 3) MD5sum: 7dd117cdf6d0c18f6d33b68bed439025 NeedsCompilation: no 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XVector Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit License: Artistic-2.0 + file LICENSE MD5sum: 94f1b6994bf05bd10a717a8bb2f30492 NeedsCompilation: yes File: rtracklayer_1.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: runibic Version: 1.28.0 Depends: R (>= 3.4.0), biclust, SummarizedExperiment Imports: Rcpp (>= 0.12.12), testthat, methods LinkingTo: Rcpp Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC License: MIT + file LICENSE MD5sum: d9cb751db1c70b5c2a16223b45ac1a61 NeedsCompilation: yes File: runibic_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: runonce Version: 0.2.3 Imports: bigassertr, urltools Suggests: testthat (>= 2.1.0), covr License: GPL-3 MD5sum: 4f0cc90ded63a45425122b521a5b0db7 NeedsCompilation: no File: runonce_0.2.3_R_x86_64-pc-linux-gnu.tar.gz Package: ruv Version: 0.9.7.1 Imports: stats, ggplot2, scales, 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spelling, testthat (>= 3.0.0), tidyverse License: GPL-3 MD5sum: 0527fe68df48cbb9ac4418086a275663 NeedsCompilation: no File: sSNAPPY_1.10.0_R_x86_64-pc-linux-gnu.tar.gz Package: sSeq Version: 1.44.0 Depends: R (>= 3.0), caTools, RColorBrewer License: GPL (>= 3) MD5sum: 4374fa983abd70cd3efab9e05f629953 NeedsCompilation: no File: sSeq_1.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: sabre Version: 0.4.3 Depends: R (>= 3.3.0) Imports: dplyr, entropy, raster, rlang, sf, tibble, tidyr Suggests: testthat, covr, knitr, rmarkdown, methods Enhances: stars, terra License: MIT + file LICENSE MD5sum: 211fd3188829fb3e8cc7a766ef2d692c NeedsCompilation: no File: sabre_0.4.3_R_x86_64-pc-linux-gnu.tar.gz Package: safe Version: 3.46.0 Depends: R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats License: GPL (>= 2) MD5sum: 593a49fd65a6dfbbffb909f33fbfe587 NeedsCompilation: no File: safe_3.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: safetensors Version: 0.1.2 Imports: cli, jsonlite, R6, rlang Suggests: testthat (>= 3.0.0), torch (>= 0.11.0) License: MIT + file LICENSE MD5sum: 50f98fef09a21532eba4e571ee52fe39 NeedsCompilation: no File: safetensors_0.1.2_R_x86_64-pc-linux-gnu.tar.gz Package: sagenhaft Version: 1.76.0 Depends: R (>= 2.10), SparseM (>= 0.73), methods Imports: graphics, stats, utils License: GPL (>= 2) MD5sum: 38725228e121de44d3d0aec7be88c9e9 NeedsCompilation: no File: sagenhaft_1.76.0_R_x86_64-pc-linux-gnu.tar.gz Package: sampleClassifierData Version: 1.30.0 Depends: R (>= 3.5.0), SummarizedExperiment Suggests: BiocStyle License: Artistic-2.0 MD5sum: d2371765278cd065165dfeb3e4d4f9bf NeedsCompilation: no File: sampleClassifierData_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: sampleClassifier Version: 1.30.0 Depends: R (>= 4.0), MGFM, MGFR, annotate Imports: e1071, ggplot2, stats, utils Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db License: Artistic-2.0 MD5sum: 3f986eed62da7c94f3315526fae6d042 NeedsCompilation: no File: sampleClassifier_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: sampling Version: 2.10 Imports: MASS, lpSolve License: GPL (>= 2) MD5sum: 8e95dfd69177628310be0ccf667414f0 NeedsCompilation: yes File: sampling_2.10_R_x86_64-pc-linux-gnu.tar.gz Package: samr Version: 3.0 Imports: impute, matrixStats, shiny, shinyFiles, openxlsx, GSA License: LGPL MD5sum: 061edbc73f4b16a1876fcc72f7ae33ab NeedsCompilation: yes File: samr_3.0_R_x86_64-pc-linux-gnu.tar.gz Package: sandwich Version: 3.1-1 Depends: R (>= 3.0.0) Imports: stats, utils, zoo Suggests: AER, car, geepack, lattice, lme4, lmtest, MASS, multiwayvcov, parallel, pcse, plm, pscl, scatterplot3d, stats4, strucchange, survival License: GPL-2 | GPL-3 MD5sum: 9dbd517a729cb33fd4fc3b084bea3ef7 NeedsCompilation: no File: sandwich_3.1-1_R_x86_64-pc-linux-gnu.tar.gz Package: sangeranalyseR Version: 1.16.0 Depends: R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER, parallel, reshape2, sangerseqR, gridExtra, shiny, shinydashboard, shinyjs, data.table, plotly, DT, zeallot, excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx, tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle, logger Suggests: testthat (>= 2.1.0) License: GPL-2 MD5sum: f1f96e9d3a39e9ced55e98f9fb856b56 NeedsCompilation: no File: sangeranalyseR_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: sangerseqR Version: 1.42.0 Depends: R (>= 3.5.0), Biostrings, pwalign, stringr Imports: methods, shiny Suggests: BiocStyle, knitr, RUnit, BiocGenerics License: GPL-2 MD5sum: 8b06bcf5b3ba3d8869671b661728d741 NeedsCompilation: no File: sangerseqR_1.42.0_R_x86_64-pc-linux-gnu.tar.gz Package: sarks Version: 1.18.0 Depends: R (>= 4.0) Imports: rJava, Biostrings, IRanges, utils, stats, cluster, binom Suggests: RUnit, BiocGenerics, ggplot2 License: BSD_3_clause + file LICENSE MD5sum: 613ced072bc5e18289349c6b636774e9 NeedsCompilation: no File: sarks_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: saseR Version: 1.2.0 Depends: R (>= 4.3.0) Imports: ASpli, S4Vectors, BiocGenerics, GenomicFeatures, MASS, PRROC, SummarizedExperiment, edgeR, pracma, precrec, BiocParallel, DESeq2, DEXSeq, data.table, limma, methods, GenomicRanges, GenomicAlignments, rrcov, MatrixGenerics, stats, IRanges, knitr, dplyr, igraph, parallel License: Artistic-2.0 MD5sum: f05241a5032b022b17044a9e10f71f2d NeedsCompilation: no File: saseR_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: satuRn Version: 1.14.0 Depends: R (>= 4.1) Imports: locfdr, SummarizedExperiment, BiocParallel, limma, pbapply, ggplot2, boot, Matrix, stats, methods, graphics Suggests: knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub, ensembldb, edgeR, DEXSeq, stageR, DelayedArray License: Artistic-2.0 MD5sum: 6527454a3fccbc2ce602ab9c12729df6 NeedsCompilation: no File: satuRn_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: scAnnotatR Version: 1.12.0 Depends: R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment Imports: dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats, e1071, ape, kernlab, AnnotationHub, utils Suggests: knitr, rmarkdown, scRNAseq, testthat License: MIT + file LICENSE MD5sum: 76cd85332b588b5a9673444cf2ea800f NeedsCompilation: no File: scAnnotatR_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scBFA Version: 1.20.0 Depends: R (>= 3.6) Imports: SingleCellExperiment, SummarizedExperiment, Seurat, MASS, zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods, Matrix Suggests: knitr, rmarkdown, testthat, Rtsne License: GPL-3 + file LICENSE MD5sum: c63991322026daf11d0ea887652926e6 NeedsCompilation: no File: scBFA_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scBubbletree Version: 1.8.0 Depends: R (>= 4.2.0) Imports: reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree, patchwork, proxy, methods, stats, base, utils, dplyr Suggests: BiocStyle, knitr, testthat, cluster, SingleCellExperiment License: GPL-3 + file LICENSE MD5sum: 371f338f549820e4d123575251f0bda7 NeedsCompilation: no File: scBubbletree_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: scCB2 Version: 1.16.0 Depends: R (>= 3.6.0) Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown License: GPL-3 MD5sum: 8fae70267c8e9e10555725e4e0f38c36 NeedsCompilation: yes File: scCB2_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: scClassify Version: 1.18.0 Depends: R (>= 4.0) Imports: S4Vectors, limma, ggraph, igraph, methods, cluster, minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix, ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo Suggests: knitr, rmarkdown, BiocStyle, pkgdown License: GPL-3 MD5sum: 7b60bd942dab298c4cac66fd57c3c89d NeedsCompilation: no File: scClassify_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: scDataviz Version: 1.16.0 Depends: R (>= 4.0), S4Vectors, SingleCellExperiment, Imports: ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales, RColorBrewer, corrplot, stats, grDevices, graphics, utils, MASS, matrixStats, methods Suggests: PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra, rmarkdown License: GPL-3 MD5sum: 3571227418738fac9dfe771b93b85c2d NeedsCompilation: no File: scDataviz_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: scDblFinder Version: 1.20.2 Depends: R (>= 4.0), SingleCellExperiment Imports: igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors, BiocSingular, S4Vectors, SummarizedExperiment, scran, scater, scuttle, bluster, methods, DelayedArray, xgboost, stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools, rtracklayer Suggests: BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize, ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans License: GPL-3 + file LICENSE MD5sum: d7855dfe5632e184b283de3a5f68498c NeedsCompilation: no File: scDblFinder_1.20.2_R_x86_64-pc-linux-gnu.tar.gz Package: scDesign3 Version: 1.4.0 Depends: R (>= 4.3.0) Imports: dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist, SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm, parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba, viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop Suggests: mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0), RefManageR, sessioninfo, BiocStyle License: MIT + file LICENSE MD5sum: b38dbcdab7debbbbfa62446275c6bb78 NeedsCompilation: no File: scDesign3_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: scDiagnostics Version: 1.0.0 Depends: R (>= 4.4.0) Imports: SingleCellExperiment, methods, isotree, ggplot2, ggridges, SummarizedExperiment, ranger, transport, speedglm, cramer, rlang, bluster, patchwork Suggests: AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq, SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 289eef297f6f4bda7589ced81826c0fc 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Package: scFeatures Version: 1.6.0 Depends: R (>= 4.2.0) Imports: DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79, EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools, msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom, tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli, SingleCellSignalR, MatrixGenerics, Seurat, DT Suggests: knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR, org.Hs.eg.db, clusterProfiler License: GPL-3 MD5sum: ac6fe3e7cf7c8274b709004b5499e73b NeedsCompilation: no File: scFeatures_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: scGPS Version: 1.20.0 Depends: R (>= 3.6), SummarizedExperiment, dynamicTreeCut, SingleCellExperiment Imports: glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1), fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel, grDevices, graphics, stats, utils, DESeq2, locfit LinkingTo: Rcpp, RcppArmadillo, RcppParallel Suggests: Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown, RColorBrewer, ReactomePA, clusterProfiler, cowplot, org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne, BiocParallel, e1071, WGCNA, devtools, DOSE License: GPL-3 MD5sum: cdd5777d9a6ac795c93e629cc2f31b48 NeedsCompilation: yes File: scGPS_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scHOT Version: 1.18.0 Depends: R (>= 4.0) Imports: S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix, SummarizedExperiment, IRanges, methods, stats, BiocParallel, reshape, ggplot2, igraph, grDevices, ggforce, graphics Suggests: knitr, markdown, rmarkdown, scater, scattermore, scales, matrixStats, deldir License: GPL-3 MD5sum: 3dacf518f4ff3071bf26016042f5189c NeedsCompilation: no File: scHOT_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: scMET Version: 1.8.0 Depends: R (>= 4.2.0) Imports: methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS, logitnorm, ggplot2, matrixStats, assertthat, viridis, coda, BiocStyle, cowplot, stats, SummarizedExperiment, SingleCellExperiment, Matrix, dplyr, S4Vectors LinkingTo: BH (>= 1.66.0), Rcpp (>= 1.0.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.21.3), StanHeaders (>= 2.21.0.7) Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: 59393c497feed9cd720e86cae2ffcbaa NeedsCompilation: yes File: scMET_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: scMerge Version: 1.22.0 Depends: R (>= 3.6.0) Imports: BiocParallel, BiocSingular, BiocNeighbors, cluster, DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>= 1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran, methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>= 1.7.3), SummarizedExperiment Suggests: BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales, proxy, testthat, badger License: GPL-3 MD5sum: 1e42b82252d644c4aa53981eb2b00469 NeedsCompilation: no File: scMerge_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: scMitoMut Version: 1.2.0 Depends: R (>= 4.3.0) Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices LinkingTo: Rcpp, RcppArmadillo Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils License: Artistic-2.0 MD5sum: 4ca5a5cbf0f89cccca56617c060fc1e9 NeedsCompilation: yes File: scMitoMut_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: scMultiSim Version: 1.2.0 Depends: R (>= 4.4.0) Imports: foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel Suggests: knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 60af5f26dee29a4477379681ca931401 NeedsCompilation: no File: scMultiSim_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: scMultiome Version: 1.6.0 Depends: AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment Imports: AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5, alabaster.matrix Suggests: BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData License: CC BY-SA 4.0 MD5sum: 6de8d02994fa53bc73bdc7350f32dd7c NeedsCompilation: no File: scMultiome_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: scPCA Version: 1.20.0 Depends: R (>= 4.0.0) Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr, Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca, cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray, ScaledMatrix, MatrixGenerics Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter, SingleCellExperiment, microbenchmark License: MIT + file LICENSE MD5sum: 0146c2ddd56a19301f2faf6097144af2 NeedsCompilation: no File: scPCA_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scPipe Version: 2.6.0 Depends: R (>= 4.2.0), SingleCellExperiment Imports: AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings, data.table, dplyr, DropletUtils, flexmix, GenomicRanges, GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices, graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0), mclust, methods, MultiAssayExperiment, org.Hs.eg.db, org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate, Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer, SummarizedExperiment, S4Vectors, scales, stats, stringr, tibble, tidyr, tools, utils, vctrs (>= 0.5.2) LinkingTo: Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat Suggests: BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra, knitr, locStra, plotly, rmarkdown, RColorBrewer, readr, reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap License: GPL (>= 2) MD5sum: 47c275b9e893649a3abe7058063cd884 NeedsCompilation: yes File: scPipe_2.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: scRNAseqApp Version: 1.6.1 Depends: R (>= 4.3.0) Imports: bibtex, bslib, circlize, ComplexHeatmap, colourpicker, data.table, DBI, DT, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales, scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager, slingshot, SingleCellExperiment, sortable, stats, tools, xfun, xml2, utils Suggests: rmarkdown, knitr, testthat, BiocStyle Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle License: GPL-3 MD5sum: 8bcf892262e03cc0748ca55af854087b NeedsCompilation: no File: scRNAseqApp_1.6.1_R_x86_64-pc-linux-gnu.tar.gz Package: scRNAseq Version: 2.20.0 Depends: SingleCellExperiment Imports: utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray, DelayedArray, GenomicRanges, SummarizedExperiment, ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6), AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base, alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite Suggests: BiocStyle, knitr, rmarkdown, testthat, jsonvalidate, BiocManager License: CC0 MD5sum: 38a446007fa84e7ed780e17c471c15cb NeedsCompilation: no File: scRNAseq_2.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scReClassify Version: 1.12.0 Depends: R (>= 4.1) Imports: randomForest, e1071, stats, SummarizedExperiment, SingleCellExperiment, methods Suggests: testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr License: GPL-3 + file LICENSE MD5sum: 0940e2d343882b6398d08043f752a652 NeedsCompilation: no File: scReClassify_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scRecover Version: 1.22.0 Depends: R (>= 3.4.0) Imports: stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>= 1.12.0) Suggests: knitr, rmarkdown, SingleCellExperiment, testthat License: GPL MD5sum: dbbad394a92f02f1c40b972487a8a786 NeedsCompilation: no File: scRecover_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: scRepertoire Version: 2.2.1 Depends: ggplot2, R (>= 4.0) Imports: assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg, Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, stringr, stringdist, SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash, purrr, lifecycle LinkingTo: Rcpp Suggests: BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales, scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr License: MIT + file LICENSE MD5sum: 9d08f1a7b0c056d9e8ce9d557afb9930 NeedsCompilation: yes File: scRepertoire_2.2.1_R_x86_64-pc-linux-gnu.tar.gz Package: scShapes Version: 1.12.0 Depends: R (>= 4.1) Imports: Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS, emdbook, magrittr, utils Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: e57585e2e3d1b1bad16507d1589adbf2 NeedsCompilation: yes File: scShapes_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scTGIF Version: 1.20.0 Depends: R (>= 3.6.0) Imports: GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly, tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr, S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor, methods, scales, msigdbr, schex, tibble, ggplot2, igraph Suggests: testthat License: Artistic-2.0 MD5sum: cc984feeb9616bba8a83ce906eef2afe NeedsCompilation: no File: scTGIF_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scTHI.data Version: 1.18.0 Depends: R (>= 4.0) License: GPL-2 MD5sum: b3d9b9308131138bf14ebe0346b02ce8 NeedsCompilation: no File: scTHI.data_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: scTHI Version: 1.18.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: e0a93121e61ad86dd91182281a3d21e7 NeedsCompilation: no File: scTHI_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: scTensor Version: 2.16.0 Depends: R (>= 4.1.0) Imports: methods, RSQLite, igraph, S4Vectors, plotly, reactome.db, AnnotationDbi, SummarizedExperiment, SingleCellExperiment, nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8), abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics, stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats, ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork, schex, ggplot2 Suggests: testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens, AnnotationHub License: Artistic-2.0 MD5sum: 35e62195f80a1884a2227bde599f9ca2 NeedsCompilation: no File: scTensor_2.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: scTreeViz Version: 1.12.0 Depends: R (>= 4.0), methods, epivizr, SummarizedExperiment Imports: data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph, clustree, scran, sys, epivizrData, epivizrServer, ggraph, scater, Seurat, SingleCellExperiment, ggplot2, stats, utils Suggests: knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s, metagenomeSeq, epivizrStandalone, GenomeInfoDb License: Artistic-2.0 MD5sum: bad78fb1ec27adff5eda3fcc10e0c8d2 NeedsCompilation: no File: scTreeViz_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scaeData Version: 1.2.0 Depends: R (>= 4.4.0) Imports: ExperimentHub Suggests: knitr, rmarkdown, markdown, SingleCellAlleleExperiment, Matrix, BiocStyle License: MIT + file LICENSE MD5sum: 7ed42e7312294dcdc1a239f1ecf04a4a NeedsCompilation: no File: scaeData_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: scales Version: 1.3.0 Depends: R (>= 3.6) Imports: cli, farver (>= 2.0.3), glue, labeling, lifecycle, munsell (>= 0.5), R6, RColorBrewer, rlang (>= 1.0.0), viridisLite Suggests: bit64, covr, dichromat, ggplot2, hms (>= 0.5.0), stringi, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 8ec5361bca2ff84d64bb9aeee92425e6 NeedsCompilation: yes File: scales_1.3.0_R_x86_64-pc-linux-gnu.tar.gz Package: scam Version: 1.2-18 Depends: R (>= 2.15.0), mgcv (>= 1.8-2) Imports: methods, stats, graphics, Matrix, splines Suggests: nlme License: GPL (>= 2) MD5sum: 72bda7ddcd3099b2597f3cd10a6f87f7 NeedsCompilation: yes File: scam_1.2-18_R_x86_64-pc-linux-gnu.tar.gz Package: scanMiRApp Version: 1.12.0 Depends: R (>= 4.0), scanMiR Imports: AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel, Biostrings, data.table, digest, DT, ensembldb, fst, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs, rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders, shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6 License: GPL-3 MD5sum: 148a8da0b91b329bb47b14fbdeed0656 NeedsCompilation: no File: scanMiRApp_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scanMiRData Version: 1.12.0 Depends: R (>= 4.0) Imports: scanMiR, utils Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 91d804bc78d8a81602b86a66878edbef NeedsCompilation: no File: scanMiRData_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scanMiR Version: 1.12.0 Depends: R (>= 4.0) Imports: Biostrings, pwalign, GenomicRanges, IRanges, data.table, BiocParallel, methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi, utils, graphics, grid, seqLogo, cowplot Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: GPL-3 MD5sum: 04d167bfdd489e6d1e8fc665bc97b54b NeedsCompilation: no File: scanMiR_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scater Version: 1.34.1 Depends: SingleCellExperiment, scuttle, ggplot2 Imports: stats, utils, methods, Matrix, BiocGenerics, S4Vectors, SummarizedExperiment, MatrixGenerics, SparseArray, DelayedArray, beachmat, BiocNeighbors, BiocSingular, BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer, RcppML, uwot, pheatmap, ggrepel, ggrastr Suggests: BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot, biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat, Biobase, scattermore License: GPL-3 MD5sum: 61d6904b3bfa2ae1c286f011cff80cdc NeedsCompilation: no File: scater_1.34.1_R_x86_64-pc-linux-gnu.tar.gz Package: scatterHatch Version: 1.12.0 Depends: R (>= 4.1) Imports: grid, ggplot2, plyr, spatstat.geom, stats, grDevices Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 6d0caabe03fdc31ce23e49e206a743e7 NeedsCompilation: no File: scatterHatch_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: scattermore Version: 1.2 Imports: ggplot2, scales, grid, grDevices, graphics Suggests: covr, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: c1a09ee2603150d965883fbeaa9e700d NeedsCompilation: yes File: scattermore_1.2_R_x86_64-pc-linux-gnu.tar.gz Package: scatterpie Version: 0.2.4 Depends: R (>= 4.1.0), ggplot2 Imports: ggforce, rlang, ggfun, stats, tidyr, dplyr, utils, yulab.utils (>= 0.1.6) Suggests: knitr, rmarkdown, prettydoc, maps, scales, cli License: Artistic-2.0 MD5sum: c6ce0867a2b873b13044a610a6f89966 NeedsCompilation: no File: scatterpie_0.2.4_R_x86_64-pc-linux-gnu.tar.gz Package: scatterplot3d Version: 0.3-44 Depends: R (>= 2.7.0) Imports: grDevices, graphics, stats License: GPL-2 MD5sum: bebfbd0a26f0f72d781dc01882146a2a NeedsCompilation: no File: scatterplot3d_0.3-44_R_x86_64-pc-linux-gnu.tar.gz Package: sccomp Version: 1.10.0 Depends: R (>= 4.2.0) Imports: instantiate (>= 0.2.3), callr, fs, stats, SeuratObject, SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr, rlang, tibble, boot, lifecycle, stats, tidyselect, utils, ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr, glue, withr, digest Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown, knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment, bayesplot, posterior License: GPL-3 MD5sum: 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NeedsCompilation: yes File: scde_2.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: scds Version: 1.22.0 Depends: R (>= 3.6.0) Imports: Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment, xgboost, methods, stats, dplyr, pROC Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown License: MIT + file LICENSE MD5sum: acded1a88407135532aa5d106022bb8d NeedsCompilation: no File: scds_1.22.0_R_x86_64-pc-linux-gnu.tar.gz Package: schex Version: 1.20.0 Depends: SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1) Imports: hexbin, stats, methods, cluster, dplyr, entropy, ggforce, grid, rlang, concaveman Suggests: ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr, TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph, scran, tibble, scuttle License: GPL-3 MD5sum: 67dd6d5a3223ffa2a8d6c92788964228 NeedsCompilation: no File: schex_1.20.0_R_x86_64-pc-linux-gnu.tar.gz Package: scico Version: 1.5.0 Depends: R (>= 2.10) Imports: scales, grDevices Suggests: ggplot2, testthat, dplyr, covr License: MIT + file LICENSE MD5sum: 75b56286fc04410cc989e13ab212c624 NeedsCompilation: no File: scico_1.5.0_R_x86_64-pc-linux-gnu.tar.gz Package: scider Version: 1.4.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, rlang, isoband, S4Vectors, grDevices Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: af183433f1f8e156f2e37e7456f1d1a6 NeedsCompilation: no File: scider_1.4.0_R_x86_64-pc-linux-gnu.tar.gz Package: scifer Version: 1.8.1 Imports: dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr, ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra, tibble, scales, rlang, flowCore, methods, basilisk, reticulate, here, utils, basilisk.utils Suggests: BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0) Enhances: parallel License: MIT + file LICENSE MD5sum: f16db196a1d2ad50729297c4b92073be NeedsCompilation: no File: scifer_1.8.1_R_x86_64-pc-linux-gnu.tar.gz Package: scmap Version: 1.28.0 Depends: R(>= 3.4) Imports: Biobase, SingleCellExperiment, SummarizedExperiment, BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy, utils, googleVis, ggplot2, methods, stats, e1071, randomForest, Rcpp (>= 0.12.12) LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, BiocStyle License: GPL-3 MD5sum: 2419e47db55d1c400c5e62df4c0dcd36 NeedsCompilation: yes File: scmap_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: scmeth Version: 1.26.0 Depends: R (>= 3.5.0) Imports: knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges, reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15), annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb, Biostrings, DT, HDF5Array (>= 1.7.5) Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes License: GPL-2 MD5sum: 8f313d1d16a2587c3431d37ed10b3ddd NeedsCompilation: no File: scmeth_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: scone Version: 1.30.0 Depends: R (>= 3.4), methods, SummarizedExperiment Imports: graphics, stats, utils, aroma.light, BiocParallel, class, cluster, compositions, diptest, edgeR, fpc, gplots, grDevices, hexbin, limma, matrixStats, mixtools, RColorBrewer, boot, rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment, DelayedMatrixStats, sparseMatrixStats Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 51f5cf681285f1d1b464237c4dc2ee73 NeedsCompilation: no File: scone_1.30.0_R_x86_64-pc-linux-gnu.tar.gz Package: scoreInvHap Version: 1.28.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 029e33c1bd080fe2cff3d891aa98170c NeedsCompilation: no File: scoreInvHap_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: scoup Version: 1.0.0 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: 496c6727294df0b7e6fb0a92de51bbac NeedsCompilation: no File: scoup_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: scp Version: 1.16.0 Depends: R (>= 4.3.0), QFeatures (>= 1.13.5) Imports: IHW, ggplot2, ggrepel, matrixStats, metapod, methods, MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer, S4Vectors, SingleCellExperiment, SummarizedExperiment, stats, utils Suggests: BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr, patchwork, preprocessCore, rmarkdown, scater, scpdata, sva, testthat, vdiffr, vsn, uwot License: Artistic-2.0 MD5sum: 28e59ea176fd48c0c1f845886c58e31a NeedsCompilation: no File: scp_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: scpdata Version: 1.13.0 Depends: R (>= 4.2.0), QFeatures, ExperimentHub Imports: utils, AnnotationHub, SingleCellExperiment, S4Vectors Suggests: scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat License: GPL-2 MD5sum: a48e9e739e2df50da45a38b1f1e0d68e NeedsCompilation: no File: scpdata_1.13.0_R_x86_64-pc-linux-gnu.tar.gz Package: scran Version: 1.34.0 Depends: SingleCellExperiment, scuttle Imports: SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel, Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph, statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular, bluster, metapod, dqrng, beachmat LinkingTo: Rcpp, beachmat, BH, dqrng, scuttle Suggests: testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats, HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, pheatmap, scater License: GPL-3 MD5sum: 7a69179e2583e890568189ee7b9ac8e5 NeedsCompilation: yes File: scran_1.34.0_R_x86_64-pc-linux-gnu.tar.gz Package: scrapper Version: 1.0.3 Imports: methods, Rcpp, beachmat (>= 2.21.6), DelayedArray, BiocNeighbors (>= 1.99.0), igraph, parallel LinkingTo: Rcpp, assorthead, beachmat, BiocNeighbors Suggests: testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics, sparseMatrixStats, Matrix, scRNAseq License: MIT + file LICENSE MD5sum: ab5636b3ed66d699b742abee812dd496 NeedsCompilation: yes File: scrapper_1.0.3_R_x86_64-pc-linux-gnu.tar.gz Package: screenCounter Version: 1.6.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, zlibbioc, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 4e50035d89b25483b47c43ea720eefec NeedsCompilation: yes File: screenCounter_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: scrime Version: 1.3.5 Imports: methods, stats, utils Suggests: MASS, RSQLite (>= 0.4-15), oligoClasses (>= 1.1.9), DBI License: GPL-2 MD5sum: 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GenomicRanges, IRanges, S4Vectors Imports: BiocParallel, Biostrings, BSgenome, ChIPseeker, cli, clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2, ggimage, graphics, grDevices, gridExtra, heatmaps, magick, methods, RColorBrewer, scales, seqArchR, seqPattern, stats, utils Suggests: BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2), covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>= 1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun License: GPL-3 MD5sum: 0a99dd021c929dd9286f289fffbcaadf NeedsCompilation: no File: seqArchRplus_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqCAT Version: 1.28.0 Depends: R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>= 1.20.3) Imports: dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>= 2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods, rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2), stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager License: MIT + file LICENCE MD5sum: 92a2a1a09fbb89dde7216da6b4dc7b15 NeedsCompilation: no File: seqCAT_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqLogo Version: 1.72.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: 22ffc3ae0e2cc8685ca0f74aea670bc3 NeedsCompilation: no File: seqLogo_1.72.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqPattern Version: 1.38.0 Depends: methods, R (>= 2.15.0) Imports: Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle Enhances: parallel License: GPL-3 MD5sum: 628be42e9237a6ce9bc3063517c4dfcb NeedsCompilation: no File: seqPattern_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqTools Version: 1.40.0 Depends: methods,utils,zlibbioc LinkingTo: zlibbioc Suggests: RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 2cbff94f3871070b3196a283d7dd7135 NeedsCompilation: yes File: seqTools_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqcombo Version: 1.28.0 Depends: R (>= 3.4.0) Imports: ggplot2, grid, igraph, utils, yulab.utils Suggests: emojifont, knitr, rmarkdown, prettydoc, tibble License: Artistic-2.0 MD5sum: 5b52c5e558b2de7b36df387c89428a34 NeedsCompilation: no File: seqcombo_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: seqinr Version: 4.2-36 Depends: R (>= 2.10.0) Imports: ade4,segmented License: GPL (>= 2) MD5sum: c4adf33acff4349e2ba53bc02d6d022a NeedsCompilation: yes File: seqinr_4.2-36_R_x86_64-pc-linux-gnu.tar.gz Package: seqmagick Version: 0.1.7 Depends: R (>= 3.6.0) Imports: Biostrings, magrittr, stats, utils, yulab.utils (> 0.1.1) Suggests: downloader, knitr, rmarkdown, GenomicAlignments, GenomicRanges, IRanges, muscle, Rsamtools, prettydoc License: Artistic-2.0 MD5sum: 4b8ebc26726655ebb8a018217dd02ae7 NeedsCompilation: no File: seqmagick_0.1.7_R_x86_64-pc-linux-gnu.tar.gz Package: seqminer Version: 9.7 Suggests: testthat, SKAT License: GPL 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ggplot2, BiocFileCache, GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2 Suggests: scales, BiocManager, knitr, DNAcopy, e1071, randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel, grDevices, KernSmooth, pals License: MIT + file LICENSE MD5sum: d8cefa057472192d46d5673b7fac1006 NeedsCompilation: no File: sesame_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: setRNG Version: 2024.2-1 Depends: R (>= 2.5.0) Imports: stats License: GPL-2 | file LICENSE MD5sum: f4c26c473f79ff430553f7f634472741 NeedsCompilation: no File: setRNG_2024.2-1_R_x86_64-pc-linux-gnu.tar.gz Package: sets Version: 1.0-25 Depends: R (>= 2.7.0) Imports: graphics,grDevices,stats,utils Suggests: proxy License: GPL-2 MD5sum: ab67e8aba37ccddfd1080bd3f0b0a008 NeedsCompilation: yes File: sets_1.0-25_R_x86_64-pc-linux-gnu.tar.gz Package: settings Version: 0.2.7 Imports: grDevices, graphics Suggests: knitr, rmarkdown, tinytest License: GPL-3 MD5sum: 0b068085dc5267fe846d876dd660b8a0 NeedsCompilation: no File: 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S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper Suggests: BiocStyle, testthat (>= 3.0.0), knitr, ggplot2 License: GPL-3 MD5sum: d865ee2c1cdf95ede312c9d3fd1d51c8 NeedsCompilation: no File: simpleSeg_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: simplifyEnrichment Version: 2.0.0 Depends: R (>= 4.0.0) Imports: simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong, digest, tm, GO.db, AnnotationDbi, slam, methods, clue, grDevices, stats, utils, cluster (>= 1.14.2), colorspace, GlobalOptions (>= 0.1.0) Suggests: knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan, igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics, flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11), shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter, gridtext, fpc License: MIT + file LICENSE MD5sum: 63bf3547e115f8b02cb6e0f4d57ef9fb NeedsCompilation: no File: simplifyEnrichment_2.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: sincell Version: 1.38.0 Depends: R (>= 3.0.2), igraph Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod LinkingTo: Rcpp Suggests: BiocStyle, knitr, biomaRt, stringr, monocle License: GPL (>= 2) MD5sum: 6071f61eb7edc9e7bd25967793edbddd NeedsCompilation: yes File: sincell_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: singleCellTK Version: 2.16.1 Depends: R (>= 4.0), SummarizedExperiment, SingleCellExperiment, DelayedArray, Biobase Imports: ape, anndata, AnnotationHub, batchelor, BiocParallel, celldex, colourpicker, colorspace, cowplot, cluster, ComplexHeatmap, data.table, DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, ensembldb, fields, ggplot2, ggplotify, ggrepel, ggtree, gridExtra, grid, GSVA (>= 1.50.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix (>= 1.6-1), matrixStats, methods, msigdbr, multtest, plotly, plyr, ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran, Seurat (>= 3.1.3), shiny, shinyjs, SingleR, stringr, SoupX, sva, reshape2, shinyalert, circlize, enrichR (>= 3.2), celda, shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools, tximport, tidyr, eds, withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown, magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang, TSCAN, TrajectoryUtils, scuttle, utils, stats, zellkonverter Suggests: testthat, Rsubread, BiocStyle, knitr, lintr, spelling, org.Mm.eg.db, kableExtra, shinythemes, shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics, RColorBrewer, fastmap (>= 1.1.0), harmony, SeuratObject, optparse License: MIT + file LICENSE MD5sum: e425ed6a3e45d97670e09d1b2565cc7f NeedsCompilation: no File: singleCellTK_2.16.1_R_x86_64-pc-linux-gnu.tar.gz Package: singscore Version: 1.26.0 Depends: R (>= 3.6) Imports: methods, stats, graphics, ggplot2, grDevices, ggrepel, GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase, BiocParallel, SummarizedExperiment, matrixStats, reshape2, S4Vectors Suggests: pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr License: GPL-3 MD5sum: e3cd07b19eb2f24f876fb0ebe401c2e9 NeedsCompilation: no File: singscore_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: sirt Version: 4.1-15 Depends: R (>= 3.5) Imports: CDM, graphics, methods, parallel, pbapply, Rcpp, stats, TAM, utils LinkingTo: pbv, Rcpp, RcppArmadillo Suggests: coda, igraph, lavaan, MASS, Matrix, miceadds, minqa, mirt, mvtnorm, nloptr, optimx, pbivnorm, pbv, psych, sfsmisc, sm, survey License: GPL (>= 2) MD5sum: 6c005499d81edcfd5510704da1d1dffd NeedsCompilation: yes File: sirt_4.1-15_R_x86_64-pc-linux-gnu.tar.gz Package: sitadela Version: 1.14.0 Depends: R (>= 4.1.0) Imports: Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges, methods, parallel, Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker, utils Suggests: BiocStyle, BSgenome, knitr, rmarkdown, RMySQL, RUnit License: Artistic-2.0 MD5sum: 76639e61e226d8c1e1bd81381859ee69 NeedsCompilation: no File: sitadela_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: sitmo Version: 2.0.2 Depends: R (>= 3.2.0) Imports: Rcpp (>= 0.12.13) LinkingTo: Rcpp Suggests: knitr, rmarkdown, ggplot2 License: MIT + file LICENSE MD5sum: 20f1324da8554181961ca97db541e21a NeedsCompilation: yes File: sitmo_2.0.2_R_x86_64-pc-linux-gnu.tar.gz Package: sizepower Version: 1.76.0 Depends: stats License: LGPL MD5sum: 65797e370b96574e7c6f90cc5aca6f96 NeedsCompilation: no File: sizepower_1.76.0_R_x86_64-pc-linux-gnu.tar.gz Package: sjlabelled Version: 1.2.0 Depends: R (>= 3.4) Imports: insight, datawizard, stats, tools, utils Suggests: dplyr, haven (>= 1.1.2), magrittr, sjmisc, sjPlot, knitr, rlang, rmarkdown, snakecase, testthat License: GPL-3 MD5sum: af364653a43fdb55cd909c95e59b4584 NeedsCompilation: no File: sjlabelled_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: sjmisc Version: 2.8.10 Depends: R (>= 3.4) Imports: dplyr, insight, datawizard, magrittr, methods, purrr, rlang, sjlabelled (>= 1.1.1), stats, tidyselect, utils Suggests: ggplot2, graphics, haven (>= 2.0.0), mice, nnet, sjPlot, sjstats, knitr, rmarkdown, stringdist, testthat, tidyr License: GPL-3 MD5sum: b0cc95fdd15eed60c29d7978c29da349 NeedsCompilation: no File: sjmisc_2.8.10_R_x86_64-pc-linux-gnu.tar.gz Package: sketchR Version: 1.2.0 Imports: basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods, reticulate, rlang, scales, stats Suggests: rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle, scran, scater, SingleR, celldex, cowplot, SummarizedExperiment, beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment License: MIT + file LICENSE MD5sum: 5ecd4aeaf22e7f3f212872fb7028add8 NeedsCompilation: no File: sketchR_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: skewr Version: 1.38.0 Depends: R (>= 3.1.1), methylumi, wateRmelon, mixsmsn, IlluminaHumanMethylation450kmanifest Imports: minfi, S4Vectors (>= 0.19.1), RColorBrewer Suggests: GEOquery, knitr, minfiData License: GPL-2 MD5sum: e0f6d16d30f6db549a8ef156d1602deb NeedsCompilation: no File: skewr_1.38.0_R_x86_64-pc-linux-gnu.tar.gz Package: skmeans Version: 0.2-18 Imports: slam (>= 0.1-31), clue (>= 0.3-39), cluster, stats, utils Enhances: Matrix, kmndirs License: GPL-2 MD5sum: 86aecac8db78632d7b71bb8591a1cba4 NeedsCompilation: no File: skmeans_0.2-18_R_x86_64-pc-linux-gnu.tar.gz Package: slalom Version: 1.28.0 Depends: R (>= 4.0) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats LinkingTo: Rcpp, RcppArmadillo, BH Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat License: GPL-2 MD5sum: df2b72665d89efe89f9fc125460a2903 NeedsCompilation: yes File: slalom_1.28.0_R_x86_64-pc-linux-gnu.tar.gz Package: slam Version: 0.1-55 Depends: R (>= 3.4.0) Imports: stats Enhances: Matrix, SparseM, spam License: GPL-2 MD5sum: 6b5f7bc7490e11d9e0b9d57dbaffad1c NeedsCompilation: yes File: slam_0.1-55_R_x86_64-pc-linux-gnu.tar.gz Package: slickR Version: 0.6.0 Depends: R (>= 3.6.0) Imports: htmltools,utils,tools,lifecycle,stats,xml2,base64enc,htmlwidgets,checkmate Suggests: jsonlite, knitr, pdftools, rmarkdown, svglite, leaflet, testthat, covr License: MIT + file LICENSE MD5sum: 9027b2975b8523f699f75192f8e51a5c NeedsCompilation: no File: slickR_0.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: slider Version: 0.3.2 Depends: R (>= 4.0.0) Imports: cli (>= 3.6.1), rlang (>= 1.1.1), vctrs (>= 0.6.3), warp LinkingTo: vctrs (>= 0.6.3) Suggests: covr, dplyr (>= 1.0.0), knitr, lubridate, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9052ec1bdc9d8de0e1fa4b3efb37f178 NeedsCompilation: yes File: slider_0.3.2_R_x86_64-pc-linux-gnu.tar.gz Package: slingshot Version: 2.14.0 Depends: R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils Imports: graphics, grDevices, igraph, matrixStats, methods, S4Vectors, SingleCellExperiment, SummarizedExperiment Suggests: BiocGenerics, BiocStyle, clusterExperiment, DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat, uwot, covr License: Artistic-2.0 MD5sum: 90a25ab8173282169010f0e4d3c1f585 NeedsCompilation: no File: slingshot_2.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: sm Version: 2.2-6.0 Depends: R (>= 3.1.0) Suggests: rgl, misc3d, interp, gam, tkrplot, rpanel (>= 1.1-4), tcltk License: GPL (>= 2) MD5sum: bbf96d29dd251e2c5bc456905b7d60a7 NeedsCompilation: yes File: sm_2.2-6.0_R_x86_64-pc-linux-gnu.tar.gz Package: smacof Version: 2.1-7 Depends: R (>= 3.5.0), plotrix, colorspace, e1071 Imports: graphics, stats, polynom, Hmisc, nnls, grDevices, MASS, weights, ellipse, wordcloud, parallel, foreach, doParallel Suggests: knitr, prefmod, MPsychoR, calibrate, ggplot2, rmarkdown License: GPL-3 MD5sum: 9f379e75e2de3a327ceee4472f8992d3 NeedsCompilation: yes File: smacof_2.1-7_R_x86_64-pc-linux-gnu.tar.gz Package: smartid Version: 1.2.0 Depends: R (>= 4.4) Imports: dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools, sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater, splatter, testthat (>= 3.0.0), tidytext, UpSetR License: MIT + file LICENSE MD5sum: d7181af3d119ba8ead864c6555ceaa16 NeedsCompilation: no File: smartid_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: smatr Version: 3.4-8 License: GPL-2 MD5sum: eef7a63d88758109d2d3d2d6def82b71 NeedsCompilation: no File: smatr_3.4-8_R_x86_64-pc-linux-gnu.tar.gz Package: smoof Version: 1.6.0.3 Depends: ParamHelpers (>= 1.8), checkmate (>= 1.1) Imports: BBmisc (>= 1.6), ggplot2 (>= 2.2.1), Rcpp (>= 0.11.0) LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, plot3D, plotly, mco, RColorBrewer, reticulate, covr License: BSD_2_clause + file LICENSE MD5sum: 472db726272a1004cf24da992884e85f NeedsCompilation: yes File: smoof_1.6.0.3_R_x86_64-pc-linux-gnu.tar.gz Package: smoothclust Version: 1.2.2 Depends: R (>= 4.4.0) Imports: SpatialExperiment, SummarizedExperiment, sparseMatrixStats, spdep, methods, utils Suggests: BiocStyle, knitr, STexampleData, scuttle, scran, scater, ggspavis, testthat License: MIT + file LICENSE MD5sum: 0e646dccd32e2bbadce60a151588e446 NeedsCompilation: no File: smoothclust_1.2.2_R_x86_64-pc-linux-gnu.tar.gz Package: smoother Version: 1.3 Depends: TTR(>= 0.22) License: GPL-2 MD5sum: f6674f95300c8a638bc98e6de20ec85b NeedsCompilation: no File: smoother_1.3_R_x86_64-pc-linux-gnu.tar.gz Package: smoothie Version: 1.0-4 Depends: R (>= 3.0.0) Suggests: SpatialVx, fields License: GPL (>= 2) MD5sum: 58e1aa3c70436c1ee562f2c18ac12cb1 NeedsCompilation: no File: smoothie_1.0-4_R_x86_64-pc-linux-gnu.tar.gz Package: smurf Version: 1.1.7 Depends: R (>= 3.4) Imports: catdata, glmnet (>= 4.0), graphics, MASS, Matrix, methods, mgcv, parallel, RColorBrewer, Rcpp (>= 0.12.12), stats LinkingTo: Rcpp, RcppArmadillo (>= 0.8.300.1.0) Suggests: bookdown, knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat License: GPL (>= 2) MD5sum: cfc8fe6d78d2a72546308f2df772eb86 NeedsCompilation: yes File: smurf_1.1.7_R_x86_64-pc-linux-gnu.tar.gz Package: sn Version: 2.1.1 Depends: R (>= 3.0.0), methods, stats4 Imports: mnormt (>= 2.0.0), numDeriv, utils, quantreg Suggests: R.rsp License: GPL-2 | GPL-3 MD5sum: a991fb7d22e5bae1605355c4c1cdeb6a NeedsCompilation: no File: sn_2.1.1_R_x86_64-pc-linux-gnu.tar.gz Package: sna Version: 2.8 Depends: R (>= 2.0.0), utils, statnet.common, network Suggests: rgl, numDeriv, SparseM License: GPL (>= 2) MD5sum: 1dae4fa7b329380a4bed0659a0900e54 NeedsCompilation: yes File: sna_2.8_R_x86_64-pc-linux-gnu.tar.gz Package: snakecase Version: 0.11.1 Depends: R (>= 3.2) Imports: stringr, stringi Suggests: testthat, covr, tibble, purrrlyr, knitr, rmarkdown, magrittr License: GPL-3 MD5sum: 047b6db51bced73bf89c69302166da8f NeedsCompilation: no File: snakecase_0.11.1_R_x86_64-pc-linux-gnu.tar.gz Package: snapcount Version: 1.18.0 Depends: R (>= 4.0.0) Imports: R6, httr, rlang, purrr, jsonlite, assertthat, data.table, Matrix, magrittr, methods, stringr, stats, IRanges, GenomicRanges, SummarizedExperiment Suggests: BiocManager, bit64, covr, knitcitations, knitr (>= 1.6), devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: da4ddd80aa8bf3d466d971576d64c16e NeedsCompilation: no File: snapcount_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: snifter Version: 1.16.0 Depends: R (>= 4.0.0) Imports: basilisk, reticulate, irlba, stats, assertthat Suggests: knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3c1db9403dac8e57c7a3ba461e1c3236 NeedsCompilation: no File: snifter_1.16.0_R_x86_64-pc-linux-gnu.tar.gz Package: snm Version: 1.54.0 Depends: R (>= 2.12.0) Imports: corpcor, lme4 (>= 1.0), splines License: LGPL MD5sum: 0885e1ebc0df3099e942fbc599014551 NeedsCompilation: no File: snm_1.54.0_R_x86_64-pc-linux-gnu.tar.gz Package: snow Version: 0.4-4 Depends: R (>= 2.13.1), utils Suggests: rlecuyer 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Imports: ggplot2, methods, stats, dplyr, spatstat.geom, spatstat.random, SpatialExperiment, SummarizedExperiment, RANN Suggests: RefManageR, BiocStyle, knitr, testthat (>= 3.0.0), sessioninfo, rmarkdown, markdown License: Artistic-2.0 MD5sum: 9726b6d9fa524bd587a881923b44af37 NeedsCompilation: no File: spaSim_1.8.0_R_x86_64-pc-linux-gnu.tar.gz Package: spacetime Version: 1.3-3 Depends: R (>= 3.0.0) Imports: graphics, utils, stats, methods, lattice, sp (>= 1.1-0), zoo (>= 1.7-9), xts (>= 0.8-8), intervals Suggests: adehabitatLT, cshapes (>= 2.0), foreign, googleVis, gstat (>= 1.0-16), maps, mapdata, plm, raster, RColorBrewer, rmarkdown, RPostgreSQL, knitr, ISOcodes, markdown, sf, sftime, spdep License: GPL (>= 2) MD5sum: 6f4ee9c46e5abe1f60987260708d6edb NeedsCompilation: no File: spacetime_1.3-3_R_x86_64-pc-linux-gnu.tar.gz Package: spam Version: 2.11-1 Depends: R (>= 4.0) Imports: dotCall64, grid, methods, Rcpp (>= 1.0.8.3) LinkingTo: Rcpp Suggests: spam64, fields, Matrix, testthat, R.rsp, truncdist, knitr, rmarkdown License: LGPL-2 | BSD_3_clause + file LICENSE MD5sum: 4619458d30afa909e4afc7e77d3adbba NeedsCompilation: yes File: spam_2.11-1_R_x86_64-pc-linux-gnu.tar.gz Package: sparcl Version: 1.0.4 License: GPL-2 MD5sum: 05a2e333f5f0afe28e22ace2c4556204 NeedsCompilation: yes File: sparcl_1.0.4_R_x86_64-pc-linux-gnu.tar.gz Package: sparkline Version: 2.0 Imports: htmltools, htmlwidgets (>= 0.8) Suggests: formattable, knitr, rmarkdown, shiny License: MIT + file LICENSE MD5sum: 2c483051d536ed35aab369a5a73d10a4 NeedsCompilation: no File: sparkline_2.0_R_x86_64-pc-linux-gnu.tar.gz Package: sparklyr Version: 1.8.6 Depends: R (>= 3.2) Imports: config (>= 0.2), DBI (>= 1.0.0), dbplyr (>= 2.5.0), dplyr (>= 1.0.9), generics, globals, glue, httr (>= 1.2.1), jsonlite (>= 1.4), methods, openssl (>= 0.8), purrr, rlang (>= 0.1.4), rstudioapi (>= 0.10), tidyr (>= 1.2.0), tidyselect, uuid, vctrs, withr, xml2 Suggests: arrow (>= 0.17.0), broom, diffobj, foreach, ggplot2, iterators, janeaustenr, Lahman, mlbench, nnet, nycflights13, R6, r2d3, RCurl, reshape2, shiny (>= 1.0.1), parsnip, testthat, rprojroot License: Apache License 2.0 | file LICENSE MD5sum: de4ff02c883c456ead089dc77cdaddce NeedsCompilation: no File: sparklyr_1.8.6_R_x86_64-pc-linux-gnu.tar.gz Package: sparrow Version: 1.12.0 Depends: R (>= 4.0) Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot License: MIT + file LICENSE MD5sum: f0939cc95ee98dbee4ab81ae2f29af7e NeedsCompilation: no File: sparrow_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: sparseMVN Version: 0.2.2 Depends: R (>= 3.4.0) Imports: Matrix (>= 1.3), methods Suggests: dplyr (>= 1.0), tidyr (>= 1.1), ggplot2 (>= 3.3), forcats (>= 0.5), mvtnorm (>= 1.0.6) , knitr, bookdown, kableExtra, testthat, scales, trustOptim (>= 0.8.5) License: MPL (>= 2.0) MD5sum: f58f3ad0e4e6bdfe2eb277efae5e42f8 NeedsCompilation: no File: sparseMVN_0.2.2_R_x86_64-pc-linux-gnu.tar.gz Package: sparseMatrixStats Version: 1.18.0 Depends: MatrixGenerics (>= 1.5.3) Imports: Rcpp, Matrix, matrixStats (>= 0.60.0), methods LinkingTo: Rcpp Suggests: testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: e709800b0ae2b736aaa4a42c4f5fe350 NeedsCompilation: yes File: sparseMatrixStats_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: sparsenetgls Version: 1.24.0 Depends: R (>= 4.0.0), Matrix, MASS Imports: methods, glmnet, huge, stats, graphics, utils Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) License: GPL-3 MD5sum: 4842d473111cc333fd425aa42fad51ea NeedsCompilation: no File: sparsenetgls_1.24.0_R_x86_64-pc-linux-gnu.tar.gz Package: sparsepca Version: 0.1.2 Imports: rsvd License: GPL (>= 3) MD5sum: 5505a7be273756ba797a250409ede3de NeedsCompilation: no File: sparsepca_0.1.2_R_x86_64-pc-linux-gnu.tar.gz Package: sparsevctrs Version: 0.2.0 Depends: R (>= 4.0.0) Imports: cli (>= 3.4.0), rlang (>= 1.1.0), vctrs Suggests: knitr, Matrix, methods, rmarkdown, testthat (>= 3.0.0), tibble, withr License: MIT + file LICENSE MD5sum: 907b95eeac5dd991ad725cd984e055fc NeedsCompilation: yes File: sparsevctrs_0.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: spatialDE Version: 1.12.0 Depends: R (>= 4.3) Imports: reticulate, basilisk (>= 1.9.10), checkmate, stats, SpatialExperiment, methods, SummarizedExperiment, Matrix, ggplot2, ggrepel, scales, gridExtra Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 9dd9dd53d3049d29fa20af3c01310f8d NeedsCompilation: no File: spatialDE_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: spatialEco Version: 2.0-2 Depends: R (>= 4.2) Imports: sf, terra Suggests: spatstat.geom (>= 3.0-3), spatstat.explore, spdep, ks, cluster, readr, RCurl, RANN, rms, yaImpute, mgcv, zyp, SpatialPack (>= 0.3), MASS, caret, dplyr, earth, Matrix, gstat, spatstat.data, methods, units, sp, stringr, lwgeom, geodata License: GPL-3 MD5sum: ef9ed3ea7f86e0cd55b77a9ff4cccfdf NeedsCompilation: no File: spatialEco_2.0-2_R_x86_64-pc-linux-gnu.tar.gz Package: spatialHeatmap Version: 2.12.1 Depends: R (>= 3.5.0) Imports: data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid, gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices, graphics, ggplotify, parallel, reshape2, stats, SummarizedExperiment, SingleCellExperiment, shinydashboard, S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2 Suggests: AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics, BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend, DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array, htmltools, htmlwidgets, kableExtra, knitr, limma, magick, memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db, org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly, rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater, scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable, Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA, xlsx, yaml License: Artistic-2.0 MD5sum: 6b8914cba10124f88c74bc5b28e913ce NeedsCompilation: no File: spatialHeatmap_2.12.1_R_x86_64-pc-linux-gnu.tar.gz Package: spatialLIBD Version: 1.18.0 Depends: SpatialExperiment (>= 1.3.3), R (>= 3.6) Imports: shiny, golem, ggplot2, cowplot, plotly, viridisLite, shinyWidgets, sessioninfo, grid, grDevices, methods, AnnotationHub, utils, png, scater, DT, ExperimentHub, RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors, IRanges, fields, benchmarkme, SingleCellExperiment, BiocFileCache, jsonlite, tibble, rtracklayer, Matrix, BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR, limma, statmod, MatrixGenerics, rlang, dplyr Suggests: knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0), covr, here, BiocManager, lobstr, DropletUtils License: Artistic-2.0 MD5sum: 6dcc129082a47fcf1acb3bca7b6f9744 NeedsCompilation: no File: spatialLIBD_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: spatialSimGP Version: 1.0.0 Depends: R (>= 4.4) Imports: SpatialExperiment, MASS, SummarizedExperiment Suggests: testthat (>= 3.0.0), STexampleData, ggplot2, knitr License: MIT + file LICENSE MD5sum: 11abd889d5bb14a5a3ec21c02d9c0358 NeedsCompilation: no File: spatialSimGP_1.0.0_R_x86_64-pc-linux-gnu.tar.gz Package: spatialreg Version: 1.3-6 Depends: R (>= 3.3.0), spData (>= 2.3.1), Matrix, sf Imports: spdep (>= 1.3-1), coda, methods, MASS, boot, splines, LearnBayes, nlme, multcomp Suggests: parallel, RSpectra, tmap, foreign, spam, knitr, lmtest, expm, sandwich, rmarkdown, igraph (>= 2.0.0), tinytest License: GPL-2 MD5sum: f5b7c331405f73c64ec2241ac10a8860 NeedsCompilation: yes File: spatialreg_1.3-6_R_x86_64-pc-linux-gnu.tar.gz Package: spatstat.data Version: 3.1-4 Depends: R (>= 3.5.0) Imports: spatstat.utils (>= 3.0-5), Matrix Suggests: spatstat.geom, spatstat.random, spatstat.explore, spatstat.model, spatstat.linnet License: GPL (>= 2) MD5sum: 9ee162434b34a19f39519fe9074fe011 NeedsCompilation: no File: spatstat.data_3.1-4_R_x86_64-pc-linux-gnu.tar.gz Package: spatstat.explore Version: 3.3-4 Depends: R (>= 3.5.0), spatstat.data (>= 3.1-2), spatstat.univar (>= 3.0-0), spatstat.geom (>= 3.3-2), spatstat.random (>= 3.3-1), stats, graphics, grDevices, utils, methods, nlme Imports: spatstat.utils (>= 3.1-0), spatstat.sparse (>= 3.1-0), goftest (>= 1.2-2), Matrix, abind Suggests: sm, gsl, locfit, spatial, fftwtools (>= 0.9-8), spatstat.linnet (>= 3.2-1), spatstat.model (>= 3.3-1), spatstat (>= 3.1-1) License: GPL (>= 2) 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GenomeInfoDb, GenomicFeatures, GenomicInteractions, GenomicRanges, ggplot2, IRanges, MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats, SummarizedExperiment, TFBSTools, utils Suggests: BiocManager, Biostrings, knitr, pheatmap, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene License: GPL-3 MD5sum: 8cf3b05d18961e98a4152a8e1aa8b955 NeedsCompilation: no File: spatzie_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: spdep Version: 1.3-10 Depends: R (>= 3.3.0), methods, spData (>= 2.3.1), sf Imports: stats, deldir, boot (>= 1.3-1), graphics, utils, grDevices, units, s2, e1071, sp (>= 1.0) Suggests: spatialreg (>= 1.2-1), Matrix, parallel, dbscan, RColorBrewer, lattice, xtable, foreign, igraph, RSpectra, knitr, classInt, tmap, spam, ggplot2, rmarkdown, tinytest, rgeoda (>= 0.0.11.1) License: GPL (>= 2) MD5sum: b5ff79527d8d3c1842f06531c02bd101 NeedsCompilation: yes File: spdep_1.3-10_R_x86_64-pc-linux-gnu.tar.gz Package: spdl Version: 0.0.5 Imports: RcppSpdlog (>= 0.0.13) License: GPL (>= 2) MD5sum: 89ef640426d8aa9f1a2ffe9fd4517480 NeedsCompilation: no File: spdl_0.0.5_R_x86_64-pc-linux-gnu.tar.gz Package: speaq Version: 2.7.0 Depends: R (>= 3.1.0), Imports: MassSpecWavelet, cluster, parallel, doSNOW, data.table, foreach, stats, Rfast, utils, graphics, grDevices, ggplot2, gridExtra, reshape2, rvest, xml2, missForest, impute Suggests: datasets, knitr, rmarkdown, grid, gridBase License: Apache License 2.0 MD5sum: 180e64e3fc5dcec823795048ecb7badf NeedsCompilation: no File: speaq_2.7.0_R_x86_64-pc-linux-gnu.tar.gz Package: specL Version: 1.40.0 Depends: R (>= 4.1), DBI (>= 0.5), methods (>= 3.3), protViz (>= 0.7), RSQLite (>= 1.1), seqinr (>= 3.3) Suggests: BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown, RUnit (>= 0.4) License: GPL-3 MD5sum: aed22629c53ee170d88ad342274d9718 NeedsCompilation: no File: specL_1.40.0_R_x86_64-pc-linux-gnu.tar.gz Package: speckle Version: 1.6.0 Depends: R (>= 4.2.0) Imports: limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods, stats, grDevices, graphics Suggests: BiocStyle, knitr, rmarkdown, statmod, CellBench, scater, patchwork, jsonlite, vdiffr, testthat (>= 3.0.0) License: GPL-3 MD5sum: 5798488ce858f3ab4edb9ca155f9daf2 NeedsCompilation: no File: speckle_1.6.0_R_x86_64-pc-linux-gnu.tar.gz Package: speedglm Version: 0.3-5 Depends: Matrix, MASS, biglm Imports: methods, stats License: GPL MD5sum: 736777b001c269a5e5fb2ee874ecad1b NeedsCompilation: no File: speedglm_0.3-5_R_x86_64-pc-linux-gnu.tar.gz Package: spelling Version: 2.3.1 Imports: commonmark, xml2, hunspell (>= 3.0), knitr Suggests: pdftools License: MIT + file LICENSE MD5sum: cc920b753d610f5f477925ddbdad3d1f NeedsCompilation: no File: spelling_2.3.1_R_x86_64-pc-linux-gnu.tar.gz Package: spicyR Version: 1.18.0 Depends: R (>= 4.1) Imports: ggplot2, concaveman, BiocParallel, spatstat.explore, spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang, grDevices, stats, data.table, dplyr, tidyr, scam, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes, ggh4x, coxme, ggnewscale Suggests: SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown, imcRtools, testthat (>= 3.0.0) License: GPL (>= 2) MD5sum: 5533ee7f8d71443278aad03e5a87f55b NeedsCompilation: no File: spicyR_1.18.0_R_x86_64-pc-linux-gnu.tar.gz Package: spikeLI Version: 2.66.0 Imports: graphics, grDevices, stats, utils License: GPL-2 MD5sum: 247f8f97693154c4d89de46b08488410 NeedsCompilation: no File: spikeLI_2.66.0_R_x86_64-pc-linux-gnu.tar.gz Package: spiky Version: 1.12.0 Depends: Rsamtools, GenomicRanges, R (>= 3.6.0) Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings, GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome, S4Vectors, graphics, ggplot2, utils Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager License: GPL-2 MD5sum: 1f918184936befcb84afc617fbbceecf NeedsCompilation: no File: spiky_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: spillR Version: 1.2.0 Depends: R (>= 4.3.0), SummarizedExperiment, CATALYST Imports: dplyr, tibble, tidyselect, stats, ggplot2, tidyr, spatstat.univar, S4Vectors, parallel Suggests: knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle, hexbin License: LGPL-3 MD5sum: 1777acd6e34bdeba688a20512102d983 NeedsCompilation: no File: spillR_1.2.0_R_x86_64-pc-linux-gnu.tar.gz Package: spkTools Version: 1.62.0 Depends: R (>= 2.7.0), Biobase (>= 2.5.5) Imports: Biobase (>= 2.5.5), graphics, grDevices, gtools, methods, RColorBrewer, stats, utils Suggests: xtable License: GPL (>= 2) MD5sum: 86b6aa2496e6517276a6b518af631211 NeedsCompilation: no File: spkTools_1.62.0_R_x86_64-pc-linux-gnu.tar.gz Package: splancs Version: 2.01-45 Depends: R (>= 2.10.0), sp (>= 0.9) Imports: stats, graphics, grDevices, methods License: 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Imports: textshape (>= 1.3.0), NLP, zoo, dtt, stats, graphics, dplyr, tidyr, rlang Suggests: devtools, knitr, pander, parallel, readxl, rmarkdown, stringr, testthat (>= 0.9.1) License: GPL-3 MD5sum: e107d5d542a1e26de3add442b3ab74c7 NeedsCompilation: no File: syuzhet_1.0.7_R_x86_64-pc-linux-gnu.tar.gz Package: tLOH Version: 1.14.0 Depends: R (>= 4.2) Imports: scales, stats, utils, ggplot2, data.table, purrr, dplyr, VariantAnnotation, GenomicRanges, MatrixGenerics, bestNormalize, depmixS4, naniar, stringr Suggests: knitr, rmarkdown License: MIT + file LICENSE MD5sum: 4715e374de9b3341a631e2d406258a3c NeedsCompilation: no File: tLOH_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: tRNA Version: 1.24.0 Depends: R (>= 3.5), GenomicRanges, Structstrings Imports: stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: 2581cad0b13af4d789582f120d89a989 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IRanges, S4Vectors, scattermore, dplyr, RColorBrewer, grDevices, stats, SummarizedExperiment, utils Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats, cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db License: GPL-3 MD5sum: 4517ba2c016bf50e233725858bb5b4c0 NeedsCompilation: no File: tricycle_1.14.0_R_x86_64-pc-linux-gnu.tar.gz Package: triebeard Version: 0.4.1 Imports: Rcpp LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 3dcb1fc5213a0d3e0c6f64c949f275b3 NeedsCompilation: yes File: triebeard_0.4.1_R_x86_64-pc-linux-gnu.tar.gz Package: trigger Version: 1.52.0 Depends: R (>= 2.14.0), corpcor, qtl Imports: qvalue, methods, graphics, sva License: GPL-3 MD5sum: 57d241a3b4365f40bec8864b99bc278d NeedsCompilation: yes File: trigger_1.52.0_R_x86_64-pc-linux-gnu.tar.gz Package: trio Version: 3.44.0 Depends: R (>= 3.0.1) Imports: grDevices, graphics, methods, stats, survival, utils, siggenes, LogicReg (>= 1.6.1) Suggests: haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth, VariantAnnotation License: LGPL-2 MD5sum: a3d65f604230214c4ca2e58586f6532d NeedsCompilation: no File: trio_3.44.0_R_x86_64-pc-linux-gnu.tar.gz Package: triplex Version: 1.46.0 Depends: R (>= 2.15.0), S4Vectors (>= 0.5.14), IRanges (>= 2.5.27), XVector (>= 0.11.6), Biostrings (>= 2.39.10) Imports: methods, grid, GenomicRanges LinkingTo: S4Vectors, IRanges, XVector, Biostrings Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer License: BSD_2_clause + file LICENSE MD5sum: 52593f968353bafbb489750223beb7ff NeedsCompilation: yes File: triplex_1.46.0_R_x86_64-pc-linux-gnu.tar.gz Package: tripr Version: 1.12.0 Depends: shiny (>= 1.6.0), shinyBS Imports: shinyjs, shinyFiles, plyr, data.table, DT, stringr, stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices, graphics, stats, utils, vegan Suggests: BiocGenerics, shinycssloaders, tidyverse, BiocManager, Biostrings, xtable, rlist, motifStack, knitr, rmarkdown, testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr Enhances: parallel License: MIT + file LICENSE MD5sum: f86ab834d00a602dbaa54a5fd4f9554f NeedsCompilation: no File: tripr_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: truncdist Version: 1.0-2 Depends: R (>= 2.0.1), stats4,evd License: GPL (>= 2) MD5sum: 1caa4e9bd200ea6e961ead809e5599b5 NeedsCompilation: no File: truncdist_1.0-2_R_x86_64-pc-linux-gnu.tar.gz Package: truncnorm Version: 1.0-9 Depends: R (>= 3.4.0) Suggests: testthat License: GPL (>= 2) MD5sum: 516c61ace92a86f96e2b86e5229dd8d7 NeedsCompilation: yes File: truncnorm_1.0-9_R_x86_64-pc-linux-gnu.tar.gz Package: trust Version: 0.1-8 Depends: R (>= 2.10.0) Imports: stats License: MIT + file LICENSE MD5sum: ee8c42a3adbe0ae5ad4f83ae6c15ae99 NeedsCompilation: no File: trust_0.1-8_R_x86_64-pc-linux-gnu.tar.gz Package: tseries Version: 0.10-58 Depends: R (>= 3.4.0) Imports: graphics, stats, utils, quadprog, zoo, 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Rcpp Suggests: knitr, rmarkdown, testthat License: GPL-3 MD5sum: 2c185ee57a6bf2405bd3067d626bb5de NeedsCompilation: yes File: veloviz_1.12.0_R_x86_64-pc-linux-gnu.tar.gz Package: venn Version: 1.12 Depends: R (>= 3.5.0) Imports: admisc (>= 0.33) Suggests: QCA (>= 3.9), ggplot2, ggpolypath License: GPL (>= 3) MD5sum: 23e25584b7fcb03f459168c6c7752cac NeedsCompilation: no File: venn_1.12_R_x86_64-pc-linux-gnu.tar.gz Package: vidger Version: 1.26.0 Depends: R (>= 3.5) Imports: Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr, RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment, tidyr, utils Suggests: BiocStyle, testthat License: GPL-3 | file LICENSE MD5sum: 881acd7017c88890f3be2ade5ed8efd0 NeedsCompilation: no File: vidger_1.26.0_R_x86_64-pc-linux-gnu.tar.gz Package: vioplot Version: 0.5.1 Depends: sm, zoo Suggests: base, ggplot2, RColorBrewer, knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: b11fe1a0b4bbf99ece630803daffb89a NeedsCompilation: no File: 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Suggests: covr, crayon, ggplot2, knitr, probably (>= 1.0.0), rmarkdown, survival (>= 3.5-0), testthat (>= 3.0.0), tidyr License: MIT + file LICENSE MD5sum: a70061e4d3cf61034593973a7b9b67d6 NeedsCompilation: yes File: yardstick_1.3.2_R_x86_64-pc-linux-gnu.tar.gz Package: yarn Version: 1.32.0 Depends: Biobase Imports: biomaRt, downloader, edgeR, gplots, graphics, limma, matrixStats, preprocessCore, readr, RColorBrewer, stats, quantro Suggests: knitr, rmarkdown, testthat (>= 0.8) License: Artistic-2.0 MD5sum: c9c85f54e960706776459e7d5b50739e NeedsCompilation: no File: yarn_1.32.0_R_x86_64-pc-linux-gnu.tar.gz Package: yeast2.db Version: 3.13.0 Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.53.2), org.Sc.sgd.db (>= 3.13.0) Imports: methods, AnnotationDbi Suggests: DBI, annotate, RUnit License: Artistic-2.0 MD5sum: 04e38ebc25fbd16ed2c82a1dd74e7e8c NeedsCompilation: no File: yeast2.db_3.13.0_R_x86_64-pc-linux-gnu.tar.gz Package: yeastCC Version: 1.46.0 Depends: Biobase (>= 2.5.5) 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