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tibble, rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2, gridExtra, utils LinkingTo: Rcpp Suggests: testthat, MASS, knitr, BiocStyle License: Apache License (== 2.0) + file LICENSE MD5sum: f95d4090335921da5d75359ed0b3578a NeedsCompilation: no Package: AMOUNTAIN Version: 1.37.0 Depends: R (>= 3.3.0) Imports: stats Suggests: BiocStyle, qgraph, knitr, rmarkdown License: GPL (>= 2) MD5sum: 21a6d4ed337216200ab6a42d135a81be NeedsCompilation: yes Package: amplican Version: 1.33.7 Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.61.1), Seqinfo, BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), data.table (>= 1.10.4-3), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) LinkingTo: 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MD5sum: cab45a511a729f05a253ffbc72d1d813 NeedsCompilation: no Package: AnnotationFilter Version: 1.35.0 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: 9f5b57383898518c51d01f700f6136e1 NeedsCompilation: no Package: AnnotationForge Version: 1.53.0 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: 76b4bc6f8e46703238b171bcd2e03445 NeedsCompilation: no Package: AnnotationHub Version: 4.1.0 Depends: BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3) Imports: utils, methods, grDevices, RSQLite, BiocManager, BiocVersion, curl, rappdirs, 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License: GPL (>= 3) MD5sum: 1531c8defcfa9caf516c07d798df14fd NeedsCompilation: no Package: aroma.light Version: 3.41.0 Depends: R (>= 2.15.2) Imports: stats, R.methodsS3 (>= 1.7.1), R.oo (>= 1.23.0), R.utils (>= 2.9.0), matrixStats (>= 0.55.0) Suggests: princurve (>= 2.1.4) License: GPL (>= 2) MD5sum: bd6a0e0820a07756aa72bc2c052c6c71 NeedsCompilation: no Package: ArrayExpress Version: 1.71.0 Depends: R (>= 2.9.0), Biobase (>= 2.4.0) Imports: oligo, limma, httr, utils, jsonlite, rlang, tools, methods Suggests: affy License: Artistic-2.0 MD5sum: 3a46e9abd050274b14d56553f8e9d7f7 NeedsCompilation: no Package: arrayQuality Version: 1.89.0 Depends: R (>= 2.2.0) Imports: graphics, grDevices, grid, gridBase, hexbin, limma, marray, methods, RColorBrewer, stats, utils Suggests: mclust, MEEBOdata, HEEBOdata License: LGPL MD5sum: e5d331db3b2e3d36ec10a3e108a88773 NeedsCompilation: no Package: arrayQualityMetrics Version: 3.67.2 Imports: affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter, 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stats, pracma, ggplot2, ggrepel, dplyr, limma, methods, rtracklayer Suggests: BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC, rmarkdown, BiocStyle License: GPL-3 MD5sum: 9d1dd85fd7eb3a6191333198eca6da0b NeedsCompilation: no Package: atena Version: 1.17.0 Depends: R (>= 4.3.0), SummarizedExperiment Imports: methods, stats, Matrix, BiocGenerics, MatrixGenerics, BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures, GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb, SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli Suggests: covr, BiocStyle, knitr, rmarkdown, RUnit, TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer License: Artistic-2.0 MD5sum: 8f1050cb5c71d209c6d481261bb828f1 NeedsCompilation: no Package: atSNP Version: 1.27.0 Depends: R (>= 3.6) Imports: BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table, ggplot2, grDevices, graphics, grid, motifStack, rappdirs, stats, testthat, utils, lifecycle LinkingTo: Rcpp Suggests: BiocStyle, knitr, rmarkdown License: GPL-2 MD5sum: d14d236565fed57aaac00224757c07b0 NeedsCompilation: yes Package: AUCell Version: 1.33.0 Imports: DelayedArray, DelayedMatrixStats, data.table, graphics, grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats, SummarizedExperiment, BiocGenerics, utils Suggests: Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery, knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne, testthat, zoo Enhances: doMC, doRNG, doParallel, foreach License: GPL-3 MD5sum: 04a6f172023878b263334b46aa09c315 NeedsCompilation: no Package: autonomics Version: 1.19.0 Depends: R (>= 4.0) Imports: abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, lme4, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, survival, tidyr, tidyselect, tools, utils, vsn Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase, BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite, knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme, OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, testthat, UniProt.ws, writexl, XML License: GPL-3 MD5sum: 9161dd139653379c9efbfcb070d08c54 NeedsCompilation: no Package: AWAggregator Version: 1.1.0 Depends: R (>= 4.5.0) Imports: dplyr, Peptides, progress, purrr, ranger, rlang, stats, stringr, tidyr, toOrdinal, utils Suggests: AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e3f62029c5b974a9bd293115864b186b NeedsCompilation: no Package: AWFisher Version: 1.25.0 Depends: R (>= 3.6) 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Depends: R (>= 4.5.0) Imports: scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD License: Artistic-2.0 MD5sum: 933c0a2dcfeeff7cd26b6045641694ad NeedsCompilation: no Package: Battlefield Version: 0.99.2 Depends: R (>= 4.6) Imports: stats, RANN, dplyr, SummarizedExperiment, methods Suggests: BiocStyle, knitr, markdown, rmarkdown, SpatialExperiment, SpatialExperimentIO, VisiumIO, ggplot2, pheatmap, pals, OSTA.data, tidyr, STexampleData, testthat (>= 3.0.0), codetools, grid, tools License: CeCILL | file LICENSE MD5sum: 197c07e59ed2322d58865ad32a69fb56 NeedsCompilation: no Package: BayesKnockdown Version: 1.37.0 Depends: R (>= 3.3) Imports: stats, Biobase License: GPL-3 MD5sum: 50ec1e6f4d738c599965b673f18fa484 NeedsCompilation: no Package: BayesSpace Version: 1.21.2 Depends: R (>= 4.0.0), SingleCellExperiment Imports: Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran, 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BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: f42892a0d8b386aa3c1a899d15e64999 NeedsCompilation: no Package: CalibraCurve Version: 1.1.3 Depends: R (>= 4.5.0) Imports: checkmate, dplyr, ggplot2, magrittr, openxlsx, scales, SummarizedExperiment, tidyr Suggests: BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo, testthat, vdiffr License: BSD 3-clause License + file LICENSE MD5sum: 2806651d372af17ccc33bda48f65f5f8 NeedsCompilation: no Package: calm Version: 1.25.0 Imports: mgcv, stats, graphics Suggests: knitr, rmarkdown License: GPL (>= 2) MD5sum: 51213860a5b5422fbfd52924d72a5ced NeedsCompilation: no Package: CaMutQC Version: 1.7.0 Depends: R (>= 4.5.0) Imports: ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr, DT, MesKit, maftools, data.table, utils, stats, methods, tidyr Suggests: knitr, rmarkdown, BiocStyle, shiny License: GPL-3 MD5sum: 2786a193cb2b8d3d3b3bce6530905441 NeedsCompilation: no Package: cancerclass Version: 1.55.0 Depends: R (>= 2.14.0), Biobase, binom, methods, stats Suggests: cancerdata License: GPL-3 MD5sum: 85ebd67557f9f541452b59f8af5cfe25 NeedsCompilation: yes Package: cardelino Version: 1.13.0 Depends: R (>= 4.2), stats Imports: combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree, Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors, utils, VariantAnnotation, vcfR Suggests: BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat, VGAM Enhances: doMC License: GPL-3 MD5sum: 66da3379e31b2c4ae57a8fa02c3e61a4 NeedsCompilation: yes Package: Cardinal Version: 3.13.0 Depends: R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics, S4Vectors, methods, stats, stats4 Imports: CardinalIO, Biobase, EBImage, graphics, grDevices, irlba, Matrix, matter (>= 2.7.10), nlme, parallel, utils Suggests: BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4, lmerTest License: Artistic-2.0 | file LICENSE MD5sum: c909bba37888bf6d397940a5f726e8d0 NeedsCompilation: no 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stats, rlang Suggests: knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown, withr, BiocStyle, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 9efa8348c3a13f83f61f202f799c6cb7 NeedsCompilation: no Package: CCAFE Version: 1.3.0 Depends: R (>= 4.4.0) Imports: dplyr, VariantAnnotation Suggests: testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges License: GPL-3 MD5sum: ce985b2be14d4e123f62ec7d72ee4d0c NeedsCompilation: no Package: ccfindR Version: 1.31.0 Depends: R (>= 3.6.0) Imports: stats, S4Vectors, utils, methods, Matrix, SummarizedExperiment, SingleCellExperiment, Rtsne, graphics, grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack (>= 0.7) LinkingTo: Rcpp, RcppEigen Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 9e36d29d8f8614fd33e678cd9e4a1ea9 NeedsCompilation: yes Package: ccImpute Version: 1.13.0 Imports: Rcpp, sparseMatrixStats, stats, BiocParallel, irlba, SingleCellExperiment, Matrix, SummarizedExperiment LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater, mclust, testthat (>= 3.0.0), splatter License: GPL-3 MD5sum: cf68af9357deb8644f5b1ae54fd808c4 NeedsCompilation: yes Package: CCPlotR Version: 1.9.1 Imports: plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph, scatterpie, circlize, ComplexHeatmap, tibble, grid, stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis, grDevices, graphics, stats, methods Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 04be4e30376346bfeb3bd9b6053cc0ab NeedsCompilation: no Package: CCPROMISE Version: 1.37.0 Depends: R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase, utils License: GPL (>= 2) MD5sum: 328de40ef9b79b4c3fd1255addbe6812 NeedsCompilation: no Package: CDI Version: 1.9.3 Depends: R(>= 3.6) Imports: matrixStats, SeuratObject, Seurat, stats, BiocParallel, ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment, SummarizedExperiment, methods Suggests: knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle License: GPL-3 + file LICENSE MD5sum: 53119bfa0d26f9ec185c17478eeb317f NeedsCompilation: no Package: celaref Version: 1.29.0 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: bc3dbc5403d7ac7dfe479412fc94b376 NeedsCompilation: no Package: celda Version: 1.27.0 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: 57e35cf1976faa4863b56633f235a1eb NeedsCompilation: yes Package: CellBarcode Version: 1.17.0 Depends: R (>= 4.1.0) Imports: methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr, ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings (>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr, Rsamtools LinkingTo: Rcpp, BH Suggests: BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown License: Artistic-2.0 MD5sum: ec5e6e402569046a7714d5076272844e NeedsCompilation: yes Package: cellbaseR Version: 1.35.0 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 (== 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LICENSE MD5sum: 3d4116a3c40211162015ffe6cc28b534 NeedsCompilation: yes Package: cellmigRation Version: 1.19.0 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: 8f90196ec53dd75ecdf4d2846ac42ae7 NeedsCompilation: no Package: CellMixS Version: 1.27.0 Depends: kSamples, R (>= 4.0) Imports: BiocNeighbors, ggplot2, scater, viridis, cowplot, SummarizedExperiment, SingleCellExperiment, tidyr, magrittr, dplyr, ggridges, stats, purrr, methods, BiocParallel, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne License: GPL (>= 2) MD5sum: d213cc834baa20828d9d31cd2dcafb9b NeedsCompilation: no Package: CellNOptR Version: 1.57.0 Depends: R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown Imports: igraph, stringi, stringr Suggests: data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics, Enhances: doParallel, foreach License: GPL-3 MD5sum: e27f946c2e55161cead57df6d5ceb218 NeedsCompilation: yes Package: cellscape Version: 1.35.0 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: f13f30f53ca9fce3a948e234abbf2257 NeedsCompilation: no Package: CellTrails Version: 1.29.0 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: 212456fa191b5860131311deb809ca4a NeedsCompilation: no Package: cellxgenedp Version: 1.15.0 Depends: R (>= 4.1.0), 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: 94ac8af3e126fa78ebf1980c64e88925 NeedsCompilation: no Package: CEMiTool Version: 1.35.0 Depends: R (>= 4.0) Imports: methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid, ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler, fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools, pracma, intergraph, grDevices, utils, network, matrixStats, ggdendro, gridExtra, gtable, fastcluster Suggests: testthat, BiocManager License: GPL-3 MD5sum: 05e5f0d620dc5b03ba6d6edb99944446 NeedsCompilation: no Package: censcyt Version: 1.19.0 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: a0ae1451d64328382fc6b069b11da4fb NeedsCompilation: no Package: ceRNAnetsim Version: 1.23.0 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: 3bb6bf8e048b68820e45041be57cc0e9 NeedsCompilation: no Package: CeTF Version: 1.23.0 Depends: R (>= 4.0) Imports: circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr, GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors, utils, methods LinkingTo: Rcpp, RcppArmadillo Suggests: airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat License: GPL-3 MD5sum: 0f269591e4796c60c8a57fbe6a498380 NeedsCompilation: yes Package: CexoR Version: 1.49.0 Depends: R (>= 4.2.0), S4Vectors, IRanges Imports: Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr, RColorBrewer, genomation Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown License: Artistic-2.0 | GPL-2 + file LICENSE MD5sum: 747246f7cc1eec9069b76350e20c71b8 NeedsCompilation: no Package: CFAssay Version: 1.45.0 Depends: R (>= 2.10.0) License: LGPL MD5sum: d5fcc9ec68d96616db6cf6048f591140 NeedsCompilation: no Package: cfdnakit Version: 1.9.0 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: 3ed281ded34fc807fd48f12ca59ca8bc NeedsCompilation: no Package: cfDNAPro Version: 1.17.1 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), 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BH Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs, png,rmarkdown, BiocManager,bibtex,codetools Enhances: ChemmineOB License: Artistic-2.0 MD5sum: 0ab1b42b0f2665deb647cf245df9c7fc NeedsCompilation: yes Package: CHETAH Version: 1.27.0 Depends: R (>= 4.2), ggplot2, SingleCellExperiment Imports: shiny, plotly, pheatmap, bioDist, dendextend, cowplot, corrplot, grDevices, stats, graphics, reshape2, S4Vectors, SummarizedExperiment Suggests: knitr, rmarkdown, Matrix, testthat, vdiffr License: file LICENSE MD5sum: 85bb55dd06ec4c9f3466d786d50c5656 NeedsCompilation: no Package: chevreulPlot Version: 1.3.0 Depends: R (>= 4.5.0), SingleCellExperiment, chevreulProcess Imports: base, cluster, clustree, ComplexHeatmap (>= 2.5.4), circlize, dplyr, EnsDb.Hsapiens.v86, forcats, fs, ggplot2, grid, plotly, purrr, S4Vectors, scales, scater, scran, scuttle, stats, stringr, tibble, tidyr, utils, wiggleplotr (>= 1.13.1), tidyselect, patchwork Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: af9a1c7b44657cfbbf6397c69c44fa61 NeedsCompilation: no Package: chevreulProcess Version: 1.3.0 Depends: R (>= 4.5.0), SingleCellExperiment, scater Imports: batchelor, bluster, circlize, cluster, DBI, dplyr, EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue, megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle, stringr, tibble, tidyr, tidyselect, utils Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 860c0f6c6af484677b45f8f5d5467d72 NeedsCompilation: no Package: chevreulShiny Version: 1.3.0 Depends: R (>= 4.5.0), SingleCellExperiment, shiny (>= 1.6.0), shinydashboard, chevreulProcess, chevreulPlot Imports: alabaster.base, clustree, ComplexHeatmap, DataEditR (>= 0.0.9), DBI, dplyr, DT, EnhancedVolcano, fs, future, ggplot2, ggplotify, grDevices, methods, patchwork, plotly, purrr, rappdirs, readr, RSQLite, S4Vectors, scales, shinyFiles, shinyhelper, shinyjs, shinyWidgets, stats, stringr, tibble, tidyr, tidyselect, utils, waiter, wiggleplotr Suggests: BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0), EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86 License: MIT + file LICENSE MD5sum: bcd86fe21673ad5240b9c32418609997 NeedsCompilation: no Package: Chicago Version: 1.39.0 Depends: R (>= 3.3.1), data.table Imports: matrixStats, MASS, Hmisc, Delaporte, methods, grDevices, graphics, stats, utils Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub License: Artistic-2.0 MD5sum: 2b2d22e729b21ecc792ad564abb0da47 NeedsCompilation: no Package: chimeraviz Version: 1.37.0 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: 45e8b0c046ec254566c003b4965d49ce NeedsCompilation: no Package: ChIPanalyser Version: 1.33.0 Depends: R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll, parallel Imports: methods, IRanges, S4Vectors,grDevices,graphics,stats,utils,rtracklayer,ROCR, BiocManager,GenomeInfoDb,RColorBrewer Suggests: BSgenome.Dmelanogaster.UCSC.dm6,knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: dd4f10fb69d19bfb77e8011cc4c26083 NeedsCompilation: no Package: chipenrich Version: 2.35.0 Depends: R (>= 3.4.0) Imports: AnnotationDbi, BiocGenerics, chipenrich.data, Seqinfo, 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 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parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.2.0) Suggests: clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene License: Artistic-2.0 MD5sum: 57a56af370968f3313c4bf098091e661 NeedsCompilation: no Package: chipseq Version: 1.61.0 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: dfd3c86cdf8059a62bb02a22670b7dfc NeedsCompilation: yes Package: ChIPseqR Version: 1.65.0 Depends: R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25) Imports: Biostrings, fBasics, 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R (>= 4.5.0) Imports: data.table, methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra Suggests: msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19), testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4), MsBackendMetaboLights (>= 1.3.1), pheatmap, vdiffr, IRanges, RColorBrewer License: Artistic-2.0 MD5sum: 4edcd03fbf4507495184921b92b1d327 NeedsCompilation: no Package: chromDraw Version: 2.41.0 Depends: R (>= 3.0.0) Imports: Rcpp (>= 0.11.1), GenomicRanges (>= 1.17.46) LinkingTo: Rcpp License: GPL-3 MD5sum: 60fc713999b3b847823cbed88289cef1 NeedsCompilation: yes Package: ChromHeatMap Version: 1.65.0 Depends: R (>= 2.9.0), BiocGenerics (>= 0.3.2), annotate (>= 1.20.0), AnnotationDbi (>= 1.4.0) Imports: Biobase (>= 2.17.8), graphics, grDevices, methods, stats, IRanges, rtracklayer, GenomicRanges Suggests: ALL, hgu95av2.db License: Artistic-2.0 MD5sum: c6360168c92bc0af1680a6accc2ca0eb NeedsCompilation: no Package: chromPlot Version: 1.39.0 Depends: stats, utils, graphics, grDevices, 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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: 79461c164ddd1b03052434895b847cb5 NeedsCompilation: no Package: CiteFuse Version: 1.23.0 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: 9c8511128a7000c6bca9e0d2c8386d5d NeedsCompilation: yes 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Depends: R (>= 4.4.0) Imports: AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, 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: 95f01b5d33672af69bdd36ac1acc9d03 NeedsCompilation: no Package: cleaver Version: 1.49.0 Depends: R (>= 3.0.0), methods, Biostrings (>= 1.29.8) Imports: S4Vectors, IRanges Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown, BRAIN, UniProt.ws (>= 2.36.5) License: GPL (>= 3) MD5sum: ad8b00fdeba10e1366f64435c4cd436f NeedsCompilation: no Package: clevRvis Version: 1.11.0 Imports: shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl, dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets, 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clusterProfiler, TCseq, org.Mm.eg.db, circlize, knitr, monocle, pheatmap, rmarkdown, Seurat, WGCNA, utils, BiocManager, S4Vectors, pheatmap, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 7115c181b3de701fbfda0df218f6e47b NeedsCompilation: no Package: ClusterJudge Version: 1.33.0 Depends: R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt License: Artistic-2.0 MD5sum: 70eddb67d3284517269228af576ab1fb NeedsCompilation: no Package: clusterProfiler Version: 4.19.7 Depends: R (>= 4.2.0) Imports: aisdk, AnnotationDbi, dplyr, enrichit (>= 0.1.1), enrichplot (>= 1.9.3), ggplot2, GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, jsonlite, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.2.3) Suggests: AnnotationHub, BiocManager, DOSE, ggtangle, readr, org.Hs.eg.db, quarto, testthat License: Artistic-2.0 MD5sum: 70cc33826628810d0ffc752f3dbcfeee 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SummarizedExperiment, SeuratObject, matrixStats, S4Vectors, proxy, httr, utils Suggests: ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel, BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr, data.table, R.utils License: MIT + file LICENSE MD5sum: 3c28de09ad65643c69e9bcaa8428ab34 NeedsCompilation: no Package: ClustIRR Version: 1.9.35 Depends: R (>= 4.3.0) Imports: grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales, msa, Biostrings, RADanalysis, ggseqlogo, rBLAST LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: BiocStyle, knitr, testthat, ggrepel, patchwork, htmlwidgets License: GPL-3 + file LICENSE MD5sum: 1f966a573334a4725cdf0e75eb28587d NeedsCompilation: yes Package: clustSIGNAL Version: 1.3.0 Depends: R (>= 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Depends: R (>= 3.5.0) Imports: BiocParallel, cluster, methods, gplots, graphics, grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea, forcats, ggplot2 LinkingTo: Rcpp, BH, testthat Suggests: testthat, knitr, rmarkdown, BiocStyle, SeuratObject, BiocFileCache, xml2 License: BSD_3_clause + file LICENSE MD5sum: 94c268cd092de6f50333d73395f54a8d NeedsCompilation: yes Package: cogena Version: 1.45.0 Depends: R (>= 3.6), cluster, ggplot2, kohonen Imports: methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools Suggests: knitr, rmarkdown (>= 2.1) License: LGPL-3 MD5sum: dd4cc7c1f93c6776e3d8606b310f1b2a NeedsCompilation: no Package: cogeqc Version: 1.15.1 Depends: R (>= 4.2.0) Imports: utils, graphics, stats, methods, reshape2, ggplot2, scales, ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite, Biostrings 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crayon, methods, xml2, microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6), digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr, foreach, doParallel, doRNG, irlba LinkingTo: Rcpp Suggests: genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE, AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree, dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot, flexclust, randomForest, e1071 License: MIT + file LICENSE MD5sum: 20843ce9380b77be116f41076ed7e7d1 NeedsCompilation: yes Package: comapr Version: 1.15.1 Depends: R (>= 4.1.0) Imports: methods, ggplot2, reshape2, dplyr, gridExtra, plotly, circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel, GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils, Matrix, grid, stats, SummarizedExperiment, plyr, Gviz Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod License: MIT + file LICENSE MD5sum: 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xml2, IRanges, Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils, BiocParallel, stringi, data.table Suggests: knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19), MsBackendMgf License: Artistic-2.0 MD5sum: e584459f3c75480f5477056c38c9dbc5 NeedsCompilation: no Package: ComPrAn Version: 1.19.0 Imports: data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr, rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio, scales, shinydashboard, shinyjs, stats, tibble, grid Suggests: testthat (>= 2.1.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: c4d8c701b36d272bd563f96778ea2932 NeedsCompilation: no Package: compSPOT Version: 1.9.0 Depends: R (>= 4.3.0) Imports: stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra, utils, data.table Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f85c93e2e0a9151706d564908155e242 NeedsCompilation: no Package: concordexR Version: 1.11.0 Depends: R (>= 4.5.0) Imports: BiocGenerics, BiocNeighbors, 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bc4e18e539da49a94c041db0cfeb72ff NeedsCompilation: no Package: CoreGx Version: 2.15.0 Depends: R (>= 4.1), BiocGenerics, SummarizedExperiment Imports: Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics, piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods, stats, utils, graphics, grDevices, lsa, data.table, crayon, glue, rlang, bench Suggests: pander, markdown, BiocStyle, rmarkdown, knitr, formatR, testthat License: GPL (>= 3) MD5sum: 5159b8b3a6f85daf9995c77d06a77a74 NeedsCompilation: no Package: Cormotif Version: 1.57.0 Depends: R (>= 2.12.0), affy, limma Imports: affy, graphics, grDevices License: GPL-2 MD5sum: b95edea7199ca8fcaefab593f96ba70e NeedsCompilation: no Package: corral Version: 1.21.0 Imports: ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix, methods, MultiAssayExperiment, pals, reshape2, SingleCellExperiment, SummarizedExperiment, transport Suggests: ade4, BiocStyle, CellBench, DuoClustering2018, knitr, rmarkdown, scater, testthat License: GPL-2 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399299ef92c09443806c74af82928591 NeedsCompilation: no Package: CRISPRball Version: 1.7.0 Depends: R (>= 4.4.0), shinyBS Imports: DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap, graphics, stats, ggplot2, plotly, shinyWidgets, shinycssloaders, shinyjqui, dittoSeq, matrixStats, colourpicker, shinyjs, circlize, PCAtools, utils, grDevices, htmlwidgets, methods Suggests: BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat (>= 3.0.0), knitr, rmarkdown License: MIT + file LICENSE MD5sum: 547c431a4e6ce86ff2b55f9c080a629e NeedsCompilation: no Package: crisprBase Version: 1.15.0 Depends: utils, methods, R (>= 4.1) Imports: BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges, S4Vectors, stringr Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: d7fd3a62d116b43345a3468752b00754 NeedsCompilation: no Package: crisprBowtie Version: 1.15.0 Depends: methods Imports: BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15), Seqinfo, GenomicRanges, IRanges, Rbowtie, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 49654eab9016658eeb5167e7e6374ecf NeedsCompilation: no Package: crisprBwa Version: 1.15.1 Depends: methods Imports: BiocGenerics, BSgenome, crisprBase (>= 0.99.15), Seqinfo, Rbwa, readr, stats, stringr, utils Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, testthat License: MIT + file LICENSE OS_type: unix MD5sum: 6637092a552e184a5ff70a787fce6ac5 NeedsCompilation: no Package: crisprScore Version: 1.15.3 Depends: R (>= 4.1), crisprScoreData (>= 1.1.3) Imports: BiocGenerics, Biostrings, IRanges, methods, randomForest, reticulate, stringr, utils, XVector Suggests: BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 367c22fb0683b66dcc0258ce8a8682a4 NeedsCompilation: no Package: CRISPRseek Version: 1.51.0 Depends: R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures Imports: parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges, BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray, Seqinfo, GenomicRanges, dplyr, keras, mltools, gtools, openxlsx, rio, rlang, stringr 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, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache, TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr License: file LICENSE MD5sum: fdb609576d212bc2d8d10022798cf7e7 NeedsCompilation: no Package: CrispRVariants Version: 1.39.0 Depends: R (>= 4.3.0), ggplot2 (>= 2.2.0) Imports: AnnotationDbi, BiocParallel, Biostrings, methods, GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices, grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>= 0.9.38), utils Suggests: BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl, rtracklayer, sangerseqR, testthat, VariantAnnotation 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Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils LinkingTo: Rhtslib, Rcpp Suggests: AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager License: GPL-3 MD5sum: bac078bef640a9d1f141ac2f833a3159 NeedsCompilation: yes Package: csdR Version: 1.17.0 Depends: R (>= 4.1.0) Imports: WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp LinkingTo: Rcpp Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr, igraph, dplyr License: GPL-3 MD5sum: 801615fa0004cc4e6bbdb70298c37751 NeedsCompilation: yes Package: CSOA Version: 1.1.7 Imports: dplyr, ggplot2, henna, kerntools, methods, paletteer, qs2, reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment, spatstat.utils, stats, textshape Suggests: BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle, stringr, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 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graphics, stats, utils, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR, clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker, plotly, heatmaply, Harman, pathview, apeglm, ashr Suggests: testthat, rmarkdown, knitr License: GPL-3 + file LICENSE MD5sum: 8d08d90c899cf57776c26143de104e17 NeedsCompilation: no Package: decemedip Version: 0.99.8 Depends: R (>= 4.5.0) Imports: bayesplot, cowplot, dplyr, GenomicRanges, ggplot2, IRanges, magrittr, Matrix, matrixStats, MEDIPS, methods, purrr, R.utils, Rcpp, RcppParallel, rlang, rstan, rstantools, S4Vectors, SummarizedExperiment LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: cdd72395cfc5d9501abea3da4ffe63cf NeedsCompilation: yes Package: DECIPHER Version: 3.7.1 Depends: R (>= 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SummarizedExperiment, tibble, utils Suggests: Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer, RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr, tidyverse License: Artistic-2.0 MD5sum: 0164bbeba0315e5dcdcbda7987b474c3 NeedsCompilation: no Package: DeeDeeExperiment Version: 1.1.5 Depends: R (>= 4.5.0), SingleCellExperiment Imports: SummarizedExperiment, methods, S4Vectors, utils, DESeq2, edgeR, limma, writexl, cli Suggests: macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db, topGO, clusterProfiler, DEFormats, ExperimentHub, scater, muscat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 54a20208cb5d6d5f99cd7b69155fa7b0 NeedsCompilation: no Package: DeepPINCS Version: 1.19.0 Depends: keras, R (>= 4.1) Imports: tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers, webchem, purrr, ttgsea, PRROC, reticulate, stats Suggests: knitr, testthat, rmarkdown License: Artistic-2.0 MD5sum: cdc1bcfc5e612ac71c275ae6491abdc3 NeedsCompilation: no Package: 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InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, Seqinfo, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, utils Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick, knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 429378c0363ff77c284384a207fbc5c8 NeedsCompilation: no Package: DEGraph Version: 1.63.0 Depends: R (>= 2.10.0), R.utils Imports: graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL, Rgraphviz, rrcov, NCIgraph Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph License: GPL-3 MD5sum: 0fa0e0914a2944bcbe49fef6e0df5d5e NeedsCompilation: no Package: DEGreport Version: 1.47.0 Depends: R (>= 4.0.0) Imports: utils, methods, Biobase, BiocGenerics, broom, circlize, ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices, knitr, logging, magrittr, psych, RColorBrewer, reshape, rlang, scales, stats, stringr, stringi, S4Vectors, SummarizedExperiment, tidyr, tibble Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown, statmod, testthat License: MIT + file LICENSE MD5sum: 5eec23ef236234e63447b45255ef150f NeedsCompilation: no Package: DEGseq Version: 1.65.0 Depends: R (>= 2.8.0), qvalue, methods Imports: graphics, grDevices, methods, stats, utils License: LGPL (>= 2) MD5sum: 027b9775449aaec08e00fbc86856dd04 NeedsCompilation: yes Package: DelayedArray Version: 0.37.1 Depends: R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>= 0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6), IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>= 1.7.5) Imports: stats Suggests: BiocParallel, HDF5Array (>= 1.17.12), genefilter, SummarizedExperiment, airway, lobstr, DelayedMatrixStats, knitr, rmarkdown, BiocStyle, RUnit License: Artistic-2.0 MD5sum: ca2ed0a89fa864c5cd40d9d365889968 NeedsCompilation: no 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grDevices, ggplot2, magrittr, mixtools, scales, pbmcapply, parallel, stats, utils Suggests: knitr, rmarkdown, testthat License: BSD_3_clause + file LICENSE MD5sum: 9633cecfae39d822c0dae420605a1737 NeedsCompilation: no Package: gemma.R Version: 3.7.1 Imports: magrittr, glue, memoise, jsonlite, data.table, rlang, lubridate, utils, stringr, SummarizedExperiment, Biobase, tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat, digest, R.utils, kableExtra, base64enc Suggests: testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2, ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap, viridis, poolr, listviewer, shiny License: Apache License (>= 2) MD5sum: a1ded30fcc331edec209e2c403b36f51 NeedsCompilation: no Package: genArise Version: 1.87.0 Depends: R (>= 1.7.1), locfit, tkrplot, methods Imports: graphics, grDevices, methods, stats, tcltk, utils, xtable License: file LICENSE License_restricts_use: yes MD5sum: 99bb258110dd7ad1db519b2f3dfe4434 NeedsCompilation: no Package: geneAttribution Version: 1.37.0 Imports: utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, Seqinfo, GenomicFeatures, IRanges, rtracklayer Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: aa33a78f30ca307d48cbf5de2a225fd8 NeedsCompilation: no Package: GeneBreak Version: 1.41.0 Depends: R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges Imports: graphics, methods License: GPL-2 MD5sum: 7c605fc2f1cb4f17bc6bfe975d0e13d2 NeedsCompilation: no Package: geneClassifiers Version: 1.35.0 Depends: R (>= 3.6.0) Imports: utils, methods, stats, Biobase, BiocGenerics Suggests: testthat License: GPL-2 MD5sum: 714a1452ddc0bad23d6a1954fbf487b2 NeedsCompilation: no Package: GeneExpressionSignature Version: 1.57.0 Depends: R (>= 4.0) Imports: Biobase, stats, methods Suggests: apcluster, GEOquery, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: 28c70f0a397421532d093bae6ecdc2d3 NeedsCompilation: no Package: genefilter Version: 1.93.0 Imports: MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase, graphics, methods, stats, survival, grDevices Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer, BiocStyle, knitr License: Artistic-2.0 MD5sum: e9d2eb55c7457e73626f6325405e75c0 NeedsCompilation: yes Package: genefu Version: 2.43.0 Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival, BiocStyle, magick, rmarkdown License: Artistic-2.0 MD5sum: 6fdcf4e2c266954136d30012cc827731 NeedsCompilation: no Package: GeneGA Version: 1.61.0 Depends: seqinr, hash, methods License: GPL-2 MD5sum: 8053f4cbb150732550ca686ba8a43173 NeedsCompilation: no Package: GeneMeta Version: 1.83.0 Depends: R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter Imports: methods, Biobase (>= 2.5.5) Suggests: RColorBrewer License: Artistic-2.0 MD5sum: a7053b2c0ee4b5bea1adff420c408548 NeedsCompilation: no Package: GeneNetworkBuilder Version: 1.53.0 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: a94f3b1ecfb877c2d0e0cfb67f00b3cc NeedsCompilation: yes Package: GeneOverlap Version: 1.47.0 Imports: stats, RColorBrewer, gplots, methods Suggests: RUnit, BiocGenerics, BiocStyle License: GPL-3 MD5sum: 5426ea20a686a4984c8389047ba4e28c NeedsCompilation: no Package: geneplast Version: 1.37.0 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: 9d8170e1053529a36c2083c93339ae32 NeedsCompilation: no Package: geneplotter Version: 1.89.0 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: 759c5a037472b2202c21ddc5323822aa NeedsCompilation: no Package: geneRecommender Version: 1.83.0 Depends: R (>= 1.8.0), Biobase (>= 1.4.22), methods Imports: Biobase, methods, stats License: GPL (>= 2) MD5sum: 4fb4422da385e1ae2a775c296158e216 NeedsCompilation: no Package: GeneRegionScan Version: 1.67.0 Depends: methods, Biobase (>= 2.5.5), Biostrings Imports: S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser, RColorBrewer, Biostrings Suggests: BSgenome, affy, AnnotationDbi License: GPL (>= 2) MD5sum: ce6133a63eeb5c5ecda6dcb9bc75528b NeedsCompilation: no Package: geneRxCluster Version: 1.47.0 Depends: GenomicRanges,IRanges Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 639a13e027653498ed62fc4781bca6ae NeedsCompilation: yes Package: GeneSelectMMD Version: 2.55.0 Depends: R (>= 2.13.2), Biobase Imports: MASS, graphics, stats, limma Suggests: ALL License: GPL (>= 2) MD5sum: b446d25177e2f54899e364cd74f1a171 NeedsCompilation: yes Package: GENESIS Version: 2.41.0 Imports: Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt, GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate, data.table, graphics, grDevices, igraph, Matrix, methods, reshape2, stats, utils Suggests: CompQuadForm, COMPoissonReg, poibin, SPAtest, survey, testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb License: GPL-3 MD5sum: 0f240ee1a66cfc1335297a2787868fb0 NeedsCompilation: yes Package: GeneStructureTools Version: 1.31.0 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: 20ceba69374ef400399403fdef0756de NeedsCompilation: no Package: geNetClassifier Version: 1.51.0 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: 8f7442cf3c646f89878b33758843c5a3 NeedsCompilation: no Package: GeneticsPed Version: 1.73.0 Depends: R (>= 2.4.0), MASS Imports: gdata, genetics Suggests: RUnit, gtools License: LGPL (>= 2.1) | file LICENSE MD5sum: 0369045502e96404cc9e6dc646884bbe NeedsCompilation: yes Package: GENIE3 Version: 1.33.0 Imports: stats, reshape2, dplyr Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods, BiocStyle License: GPL (>= 2) MD5sum: 5bd3bffb0b9a9c2738e0b4dfdad333a5 NeedsCompilation: yes Package: genomation Version: 1.43.0 Depends: R (>= 3.5.0), grid Imports: Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table, Seqinfo, 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: 6e278648d2d98bd2e1637d1f6ffc26b5 NeedsCompilation: yes Package: GenomAutomorphism Version: 1.13.0 Depends: R (>= 4.4.0), Imports: Biostrings, BiocGenerics, BiocParallel, Seqinfo, 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: e51643e2215459cf1177fdb09a823033 NeedsCompilation: no Package: GenomeInfoDb Version: 1.47.2 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6), IRanges (>= 2.41.1), Seqinfo (>= 0.99.2) Imports: stats, utils, UCSC.utils Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, 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: 56254f4e77ce0ed3b6443e6bf756129d NeedsCompilation: no Package: genomeIntervals Version: 1.67.0 Depends: R (>= 2.15.0), methods, intervals (>= 0.14.0), BiocGenerics (>= 0.15.2) Imports: Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14), S4Vectors (>= 0.7.10) License: Artistic-2.0 MD5sum: 22f078bdafd497bcee9c2f0f96098989 NeedsCompilation: no Package: genomes Version: 3.41.0 Depends: readr, curl License: GPL-3 MD5sum: 74b3d52fdd9c1d94898479021b04c21a NeedsCompilation: no Package: GenomicAlignments Version: 1.47.0 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>= 0.47.6), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2), Rsamtools (>= 2.25.1) Imports: methods, utils, stats, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings, Rsamtools, BiocParallel, cigarillo (>= 0.99.2) 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: 3d2c900384c04c0fb401c6b97fdb54f3 NeedsCompilation: yes Package: GenomicCoordinates Version: 0.99.3 Depends: R (>= 4.5), GenomicRanges, IRanges Imports: S4Vectors, Seqinfo, InteractionSet, methods, plyranges, plyinteractions Suggests: testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: b06b17f3b6d12d30ce873cdc7909f3ee NeedsCompilation: no Package: GenomicDataCommons Version: 1.35.1 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: ee05183e0ab26c686dd4f6ad6efc1f52 NeedsCompilation: no Package: GenomicDistributions Version: 1.19.0 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: c29a5d53ca287700155bd9e1756d1295 NeedsCompilation: no Package: GenomicFeatures Version: 1.63.2 Depends: R (>= 3.5.0), BiocGenerics (>= 0.51.2), S4Vectors (>= 0.47.6), IRanges (>= 2.37.1), Seqinfo (>= 0.99.2), GenomicRanges (>= 1.61.1), AnnotationDbi (>= 1.41.4) Imports: methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2), rtracklayer (>= 1.69.1) LinkingTo: S4Vectors, IRanges Suggests: GenomeInfoDb, 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), 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), ensembldb, AnnotationFilter, RUnit, BiocStyle, knitr, markdown License: Artistic-2.0 MD5sum: 2f0f608b4d702be7a0061c9a18e2c0fc NeedsCompilation: yes Package: GenomicFiles Version: 1.47.0 Depends: BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1) Imports: BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>= 1.55.1) Suggests: BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats License: Artistic-2.0 MD5sum: 2409acead52b919cfeaf91ae2fe39918 NeedsCompilation: no Package: genomicInstability Version: 1.17.0 Depends: R (>= 4.1.0), checkmate Imports: mixtools, SummarizedExperiment Suggests: SingleCellExperiment, ExperimentHub, pROC License: file LICENSE MD5sum: 144e2aed86a3f7e33aea86ae09cc876d NeedsCompilation: no Package: GenomicInteractionNodes Version: 1.15.0 Depends: R (>= 4.2.0), stats Imports: AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures, Seqinfo, methods, IRanges, RBGL, S4Vectors Suggests: RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db License: file LICENSE MD5sum: f7f6c0c1613bbda51c6eb2ded8b545c4 NeedsCompilation: no Package: GenomicInteractions Version: 1.45.0 Depends: R (>= 3.5), InteractionSet Imports: Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges, BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo, 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: 33d60b277ed3be3192635c276e6b0922 NeedsCompilation: no Package: GenomicRanges Version: 1.63.2 Depends: R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.45.2), IRanges (>= 2.43.6), Seqinfo (>= 0.99.3) Imports: utils, stats Suggests: GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, UCSC.utils, txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart51, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: ef92284ecbd334f9d6c10ec509f9ad51 NeedsCompilation: no Package: GenomicSuperSignature Version: 1.19.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr, dplyr, plotly, BiocFileCache, grid, flextable, irlba Suggests: knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis, BiocStyle, testthat, forcats, stats, wordcloud, circlize, EnrichmentBrowser, clusterProfiler, msigdbr, cluster, RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr, utils License: Artistic-2.0 MD5sum: 07fd3665acde756868c8d2849f6411a6 NeedsCompilation: no Package: GenomicTuples Version: 1.45.0 Depends: R (>= 4.0), GenomicRanges (>= 1.37.4), Seqinfo, S4Vectors (>= 0.17.25) Imports: methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges (>= 2.19.13), data.table, stats4, stats, utils LinkingTo: Rcpp Suggests: testthat, knitr, BiocStyle, rmarkdown, covr, GenomicAlignments, Biostrings, GenomeInfoDb License: Artistic-2.0 MD5sum: f33ffefa63cb9aa728c7ea9e82873301 NeedsCompilation: yes Package: GenProSeq Version: 1.15.0 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: 6f8e8d0a2ffd3af3a20de2378ec0cc80 NeedsCompilation: no Package: GenVisR Version: 1.43.1 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, Seqinfo, 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: 03e2e64442f4fa88e605222b971f06ea NeedsCompilation: no Package: GeoDiff Version: 1.17.0 Depends: R (>= 4.1.0), Biobase Imports: Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods, graphics, stats, testthat, GeomxTools, NanoStringNCTools LinkingTo: Rcpp, RcppArmadillo, roptim Suggests: knitr, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 6412159ed89097f05e11fdb2bdf7f658 NeedsCompilation: yes Package: GEOfastq Version: 1.19.0 Imports: xml2, rvest, stringr, RCurl, doParallel, foreach, plyr Suggests: BiocCheck, roxygen2, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: b079bba46114499a64be6136cc33b83d NeedsCompilation: no Package: GEOmetadb Version: 1.73.2 Depends: R.utils,RSQLite Suggests: knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud License: Artistic-2.0 MD5sum: 567d565237d60035d8aa63d752b03cde NeedsCompilation: no Package: GeomxTools Version: 3.15.0 Depends: R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors Imports: BiocGenerics, rjson, readxl, EnvStats, reshape2, methods, utils, stats, data.table, lmerTest, dplyr, stringr, grDevices, graphics, GGally, rlang, ggplot2, SeuratObject Suggests: rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph, Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork License: MIT MD5sum: 5ac0fbaa6cb56e9b5a124e9b2528c97f NeedsCompilation: no Package: GEOquery 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GenomicRanges, readr, cmdfun, dplyr, magrittr Suggests: covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer, derfinder, GenomeInfoDb, tools, RefManageR, testthat License: Artistic-2.0 MD5sum: fe3b333c4bae579b37cdd8349ef4a848 NeedsCompilation: no Package: MEIGOR Version: 1.45.0 Depends: R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode Suggests: CellNOptR, knitr, BiocStyle License: GPL-3 MD5sum: 30f95a675485e842b90ab7ecec7db830 NeedsCompilation: no Package: MeLSI Version: 0.99.9 Depends: R (>= 4.5.0) Imports: vegan, ggplot2, phyloseq, stats, utils Suggests: testthat, knitr, rmarkdown, BiocManager, BiocStyle, BiocParallel, Matrix, microbiome License: MIT + file LICENSE MD5sum: 5a72bbb6f13db5229dcdf888ea805136 NeedsCompilation: no Package: memes Version: 1.19.1 Depends: R (>= 4.1) Imports: Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2, magrittr, matrixStats, methods, patchwork, processx, purrr, rlang, readr, stats, tools, tibble, tidyr, utils, usethis, universalmotif (>= 1.9.3), xml2 Suggests: cowplot, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0), knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1), rmarkdown, covr License: MIT + file LICENSE MD5sum: e285f59dbd190fba048058c8c8a1c61b NeedsCompilation: no Package: Mergeomics Version: 1.39.0 Depends: R (>= 3.0.1) Suggests: RUnit, BiocGenerics License: GPL (>= 2) MD5sum: 4fef8c54f5b17b525ac8e654a1230c05 NeedsCompilation: no Package: MeSHDbi Version: 1.47.0 Depends: R (>= 3.0.1) Imports: methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase Suggests: testthat License: Artistic-2.0 MD5sum: 57172ad39951568ad87a00f54b551d9f NeedsCompilation: no Package: meshes Version: 1.37.1 Depends: R (>= 4.1.0) Imports: enrichit, gson, AnnotationDbi, GOSemSim (> 2.37.0), methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5) Suggests: knitr, rmarkdown, prettydoc License: Artistic-2.0 MD5sum: 0d9c4376e0c9627c69a2d699de7b9559 NeedsCompilation: no Package: 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dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils, rlang, graphics, matrixStats, tidyr Suggests: knitr, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 39148e0704552969870c8df5166c4feb NeedsCompilation: yes Package: metabinR Version: 1.13.0 Depends: R (>= 4.3) Imports: methods, rJava Suggests: BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) License: GPL-3 MD5sum: e8903ca17a0bafe56e43f5932cc5a20b NeedsCompilation: no Package: MetaboAnnotation Version: 1.15.3 Depends: R (>= 4.0.0) Imports: BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra (>= 1.21.5), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb Suggests: testthat, knitr, MsDataHub, BiocStyle, rmarkdown, plotly, shiny, shinyjs, msentropy, DT, microbenchmark, mzR Enhances: RMariaDB, RSQLite License: Artistic-2.0 MD5sum: 78518e564dddd4da386f55fa26588ebc NeedsCompilation: no 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utils Suggests: BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown, structToolbox, testthat, pmp, grid, png License: GPL-3 MD5sum: 3c6284f86cd2cb44d004536bd2dc6346 NeedsCompilation: no Package: metabomxtr Version: 1.45.0 Depends: methods,Biobase Imports: optimx, Formula, plyr, multtest, BiocParallel, ggplot2 Suggests: xtable, reshape2 License: GPL-2 MD5sum: 48e50d23ef07a4c0520869248ae60e53 NeedsCompilation: no Package: metaCCA Version: 1.39.0 Suggests: knitr License: MIT + file LICENSE MD5sum: c476e41d46c6e320c9f4abf608d48560 NeedsCompilation: no Package: MetaCyto Version: 1.33.0 Depends: R (>= 3.4) Imports: flowCore (>= 1.4),tidyr (>= 0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices, graphics, stats, utils Suggests: knitr, dplyr, rmarkdown License: GPL (>= 2) MD5sum: 4ab4fd7a92288dd813a614b12b6ee142 NeedsCompilation: no Package: MetaDICT Version: 1.1.0 Depends: R (>= 4.2.0) Imports: stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis, ggpubr, ape, cluster, matrixStats Suggests: BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 74bd1af23c04cf0acfa320550a347b1c NeedsCompilation: no Package: metagene2 Version: 1.27.0 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: d70173d7d1d621add51d85b03976a920 NeedsCompilation: no Package: metagenomeSeq Version: 1.53.2 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, IHW, SparseArray License: Artistic-2.0 MD5sum: 678af87b3840389225e198c4365eecb2 NeedsCompilation: no Package: metahdep Version: 1.69.0 Depends: R (>= 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methylInheritance License: Artistic-2.0 MD5sum: 8f5265aa360913293aaab325b0cc0b0c NeedsCompilation: no Package: MethPed Version: 1.39.0 Depends: R (>= 3.0.0), Biobase Imports: randomForest, grDevices, graphics, stats Suggests: BiocStyle, knitr, markdown, impute License: GPL-2 MD5sum: 3074288953afb44cf30839e47d8bb6e2 NeedsCompilation: no Package: MethTargetedNGS Version: 1.43.0 Depends: R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign Imports: utils, graphics, stats License: Artistic-2.0 MD5sum: e7e7e7f05be0b8ae129e322de235dfe4 NeedsCompilation: no Package: methyLImp2 Version: 1.7.1 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: 101ab6be3d5bfd1ef140a65abc816354 NeedsCompilation: no Package: methylInheritance Version: 1.35.0 Depends: R (>= 3.5) Imports: methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors, methods, parallel, ggplot2, gridExtra, rebus Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 99738d18c432241a98b4dd1d65015c78 NeedsCompilation: no Package: methylKit Version: 1.37.0 Depends: R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods Imports: IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>= 0.13.13), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools, gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils, limma, grDevices, graphics, stats, utils LinkingTo: Rcpp, Rhtslib (>= 1.13.1) Suggests: testthat (>= 2.1.0), knitr, rmarkdown, genomation, BiocManager License: Artistic-2.0 MD5sum: 8447b5c8866871a302b3c395812a5c5b NeedsCompilation: yes Package: MethylMix Version: 2.41.0 Depends: R (>= 3.2.0) Imports: foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute, data.table, limma, R.matlab, digest Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown License: GPL-2 MD5sum: 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httptest, knitr, rmarkdown, testthat (>= 3.0.0), rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache, msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick, structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx, ggplotify, cowplot License: GPL-3 MD5sum: 50b9657662daaf847c6e8a065b2ebc00 NeedsCompilation: no Package: MetNet Version: 1.29.0 Depends: R (>= 4.1), S4Vectors (>= 0.28.1), SummarizedExperiment (>= 1.20.0) Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>= 1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>= 1.2.15), GENIE3 (>= 1.7.0), methods (>= 4.1), parmigene (>= 1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6), stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>= 4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>= 1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>= 1.6.0) License: 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RSQLite, GO.db, testthat License: Artistic-2.0 MD5sum: bef2c3332c437ed3625efe9af5a66b93 NeedsCompilation: yes Package: mia Version: 1.19.8 Depends: R (>= 4.1.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3) Imports: ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, methods, ecodive, rlang, S4Vectors, scater, stats, stringr, tibble, tidyr, utils, vegan, Rcpp LinkingTo: Rcpp Suggests: ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaTime, miaViz, microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist, rhdf5, rmarkdown, scuttle, testthat, topicdoc, topicmodels, yaml License: Artistic-2.0 | file LICENSE MD5sum: 9663908445760124243e74aa7310a39c NeedsCompilation: yes Package: miaDash Version: 1.3.0 Depends: R (>= 4.4.0), iSEE (>= 2.19.4), shiny Imports: ape, bluster, htmltools, iSEEtree (>= 1.1.4), mia, rintrojs, scater, scuttle, shinydashboard, shinyjs, shinyWidgets, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, utils, vegan Suggests: BiocStyle, knitr, philr, remotes, rmarkdown, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: 7a35209a5b31e35e0818daa52ec85ea4 NeedsCompilation: no Package: miaSim Version: 1.17.0 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: b7e8be2e41ac8f5feb553b9baa683818 NeedsCompilation: no Package: miaTime Version: 1.1.0 Depends: R (>= 4.5.0), mia Imports: dplyr, methods, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, TreeSummarizedExperiment Suggests: BiocStyle, devtools, ggplot2, knitr, lubridate, miaViz, rmarkdown, scater, testthat, vegan License: Artistic-2.0 | file LICENSE MD5sum: 598bc71bc15d17a77a0943d8e64e8668 NeedsCompilation: no Package: miaViz Version: 1.19.6 Depends: R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment Imports: ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, methods, patchwork, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis Suggests: beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor License: Artistic-2.0 | file LICENSE MD5sum: dc984b9987ae4d3cd0ea146e17507bca NeedsCompilation: no Package: MiChip Version: 1.65.0 Depends: R (>= 2.3.0), Biobase Imports: Biobase License: GPL (>= 2) MD5sum: c83eb1f6b65ea0deb65f94cc14920554 NeedsCompilation: no Package: microbiome Version: 1.33.0 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: 68bcb9105592cd21af704ea12e9ffdb9 NeedsCompilation: no Package: microbiomeDASim Version: 1.25.0 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: bb347bd5a54963ac51a63afcbd12bbd8 NeedsCompilation: no Package: microbiomeExplorer Version: 1.21.0 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: e3b7f083777e59c406ca5285523a2c78 NeedsCompilation: no Package: MicrobiomeProfiler Version: 1.17.1 Depends: R (>= 4.2.0) Imports: enrichit, config, DT, enrichplot, golem, gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader, htmltools, ggplot2, graphics, stats, utils, yulab.utils Suggests: clusterProfiler (>= 4.5.2), rmarkdown, knitr, testthat (>= 3.0.0), prettydoc License: GPL-2 MD5sum: 28ff467406b69a03fbb34c141a96ac8e NeedsCompilation: no Package: MicrobiotaProcess Version: 1.23.1 Depends: R (>= 4.0.0) Imports: ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel, vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang, tibble, grDevices, stats, utils, coin, ggsignif, patchwork, ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>= 1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table, ggfun (>= 0.1.1) Suggests: rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, DECIPHER, randomForest, jsonlite, biomformat, scales, yaml, withr, S4Vectors, purrr, seqmagick, glue, ggupset, ggVennDiagram, ggalluvial (>= 0.11.1), forcats, phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext, DirichletMultinomial, ggpp, BiocManager, rhdf5 License: GPL (>= 3.0) MD5sum: bd690ded496bf72047e6195f0931a049 NeedsCompilation: no Package: microRNA Version: 1.69.0 Depends: R (>= 2.10) Imports: Biostrings (>= 2.11.32) License: Artistic-2.0 MD5sum: d673fb2a49d8f6686a5962a4e93b7270 NeedsCompilation: yes Package: MICSQTL Version: 1.9.0 Depends: R (>= 4.3.0), SummarizedExperiment, stats Imports: TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2, ggpubr, ggridges, glue, S4Vectors, dirmult Suggests: testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle License: GPL-3 MD5sum: c59a64c54ad8b17faf4381431876026f NeedsCompilation: no Package: midasHLA Version: 1.19.0 Depends: R (>= 4.1), MultiAssayExperiment (>= 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ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv LinkingTo: Rcpp, RcppArmadillo 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: d2f349ccd6ee448d9ae21f38772cf2ab NeedsCompilation: yes Package: mimager Version: 1.35.0 Depends: Biobase Imports: BiocGenerics, S4Vectors, preprocessCore, grDevices, methods, grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 License: MIT + file LICENSE MD5sum: 27dee40e8f6d4ea72df186a82b63b752 NeedsCompilation: no Package: mina Version: 1.19.0 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: e5e1c249bcc9803198fbf8b6542f88ae NeedsCompilation: yes Package: minet Version: 3.69.0 Imports: infotheo License: Artistic-2.0 MD5sum: d7d46c7ca683beba67ad1b01425dc178 NeedsCompilation: yes Package: MinimumDistance Version: 1.55.0 Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1) Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>= 0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16), SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff, foreach, matrixStats, lattice, data.table, grid, stats, utils Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, RUnit Enhances: snow, doSNOW License: Artistic-2.0 MD5sum: f5a138ec1b067c54c628f54b3cd2bea9 NeedsCompilation: no Package: MiPP Version: 1.83.0 Depends: R (>= 2.4) Imports: Biobase, e1071, MASS, stats License: GPL (>= 2) MD5sum: b3cc5487b257ee8d53ff2f2edfc1d8f7 NeedsCompilation: no Package: miQC Version: 1.19.0 Depends: R (>= 3.5.0) Imports: SingleCellExperiment, flexmix, ggplot2, splines Suggests: scRNAseq, scater, BiocStyle, knitr, rmarkdown License: BSD_3_clause + file LICENSE MD5sum: 66e5ee59125881db7d5773119706f9dc NeedsCompilation: no Package: MiRaGE Version: 1.53.0 Depends: R (>= 3.1.0), Biobase(>= 2.23.3) Imports: BiocGenerics, S4Vectors, AnnotationDbi, BiocManager Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData License: GPL MD5sum: 8594eaf773532cd0ef5b46f5885d89fd NeedsCompilation: no Package: miRBaseConverter Version: 1.35.0 Depends: R (>= 3.4) Imports: stats Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown License: GPL (>= 2) MD5sum: 2b01d99332cabcecf482821d44c856fa NeedsCompilation: no Package: miRcomp Version: 1.41.0 Depends: R (>= 3.5.0), Biobase (>= 2.22.0), miRcompData Imports: utils, methods, graphics, KernSmooth, stats Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny License: GPL-3 | file LICENSE MD5sum: 3db22f6381ae52559e0402c8db64ae33 NeedsCompilation: no Package: mirIntegrator Version: 1.41.0 Depends: R (>= 3.3) Imports: graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi, Rgraphviz Suggests: RUnit, BiocGenerics License: GPL (>= 3) MD5sum: 0a1d18f4edbc365e386de038899fe85a NeedsCompilation: no Package: MIRit Version: 1.7.4 Depends: MultiAssayExperiment, R (>= 4.4.0) Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils LinkingTo: Rcpp Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) License: GPL (>= 3) MD5sum: e39606bce7cb6875a74aa88bc710c4a9 NeedsCompilation: yes Package: miRNAmeConverter Version: 1.39.0 Depends: miRBaseVersions.db Imports: DBI, AnnotationDbi, reshape2 Suggests: methods, testthat, knitr, rmarkdown License: Artistic-2.0 MD5sum: 30c45948231641ec73f46cbee561a1c4 NeedsCompilation: no Package: miRNApath Version: 1.71.0 Depends: methods, R(>= 2.7.0) License: LGPL-2.1 MD5sum: 06f872eed90e3fbf71d2e26b642add6f NeedsCompilation: no Package: miRNAtap Version: 1.45.0 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: 02affb1ce40a2a68bee63cedb7cf81c7 NeedsCompilation: no Package: miRSM Version: 2.7.1 Depends: R (>= 4.4.0) Imports: WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer, grid, MCL, fabia, NMF, BicARE, isa2, methods, rJava, Biobase, PMA, stats, dbscan, 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: 8c1db4e1edbfb8c51f4246dfa6aca5bb NeedsCompilation: yes Package: mirTarRnaSeq Version: 1.19.0 Depends: R (>= 4.1.0), ggplot2 Imports: purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap, reshape2, corrplot, grDevices, graphics, stats, utils, data.table, R.utils, viridis Suggests: BiocStyle, knitr, rmarkdown, R.cache, SPONGE License: MIT + file LICENSE MD5sum: 4b2bc6d7e7457ef126ba1ba3729270ba NeedsCompilation: no Package: missRows Version: 1.31.0 Depends: R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment Imports: plyr, stats, gtools, S4Vectors Suggests: BiocStyle, knitr, testthat License: Artistic-2.0 MD5sum: 01bbfc07993b502dba9fb5feb4fe6e61 NeedsCompilation: no Package: mist Version: 1.3.3 Depends: R (>= 4.5.0) Imports: BiocParallel, MCMCpack, Matrix, S4Vectors, methods, rtracklayer, car, mvtnorm, SummarizedExperiment, SingleCellExperiment, BiocGenerics, stats, rlang Suggests: knitr, rmarkdown, RUnit, ggplot2, BiocStyle License: MIT + file LICENSE MD5sum: 738f73157785123f66cc6c0ab839d071 NeedsCompilation: no Package: mistyR Version: 1.19.0 Depends: R (>= 4.0) Imports: assertthat, caret, deldir, digest, distances, dplyr (>= 1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr, ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats, stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr Suggests: BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml, kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0), xgboost License: GPL-3 MD5sum: f307eeef454bffa9ac5b3f4c9747ff13 NeedsCompilation: no Package: mitch Version: 1.23.1 Depends: R (>= 4.4) Imports: stats, grDevices, graphics, utils, MASS, plyr, reshape2, parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2, gplots, beeswarm, echarts4r, kableExtra, dplyr, network Suggests: stringi, testthat (>= 2.1.0), HGNChelper, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 License: CC BY-SA 4.0 + file LICENSE MD5sum: 03bdf157d761705292413a529ede0ea9 NeedsCompilation: no Package: mitoClone2 Version: 1.17.0 Depends: R (>= 4.4.0) Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 LinkingTo: Rhtslib (>= 1.13.1) Suggests: knitr, rmarkdown, Biostrings, testthat License: GPL-3 MD5sum: 74392aa181b4527dfa96964f0ad0da41 NeedsCompilation: yes Package: mitology Version: 1.3.0 Depends: R (>= 4.5.0) Imports: AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap, ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales Suggests: Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr, SummarizedExperiment, testthat License: AGPL-3 MD5sum: 0138c33183893b43d71123695f9cd669 NeedsCompilation: no Package: mixOmics Version: 6.35.2 Depends: R (>= 4.4.0), MASS, lattice, ggplot2 Imports: igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr, tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra, grDevices, graphics, stats, ggrepel, BiocParallel, utils, rgl, rlang Suggests: BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark, magick, vdiffr, kableExtra, devtools License: GPL (>= 2) MD5sum: 9c7fe1444fdb3b8f22e91c2c060a381d NeedsCompilation: no Package: MLInterfaces Version: 1.91.0 Depends: R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase, annotate, cluster Imports: gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis, shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench, stats4, tools, grDevices, graphics, stats, magrittr, SummarizedExperiment Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party, klaR, BiocStyle, knitr, testthat, airway Enhances: parallel License: LGPL MD5sum: 57ababfa8ff20138dcc0d0334bc6a9f3 NeedsCompilation: no Package: MLP Version: 1.59.0 Imports: AnnotationDbi, gplots, graphics, stats, utils Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz, GOstats, graph, limma, mouse4302.db, reactome.db License: GPL-3 MD5sum: a4263c4824e00cc4e123e4022d27894a NeedsCompilation: no Package: MLSeq Version: 2.29.0 Depends: caret, ggplot2 Imports: testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq, xtable Suggests: knitr, e1071, kernlab License: GPL (>= 2) MD5sum: 74fa89770ef17948fe0e74fbf09bc4e9 NeedsCompilation: no Package: MMDiff2 Version: 1.39.0 Depends: R (>= 3.5.0), Rsamtools, Biobase Imports: GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2, RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 License: Artistic-2.0 MD5sum: 60df2fc40d79d08ff68c589d418dabde NeedsCompilation: no Package: MMUPHin Version: 1.99.3 Depends: R (>= 3.6) Imports: maaslin3, metafor, fpc, igraph, ggplot2, dplyr, tidyr, stringr, cowplot, utils, stats, grDevices Suggests: testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan, phyloseq, curatedMetagenomicData, genefilter License: MIT + file LICENSE MD5sum: 2aa95026e432076e4e66c81c3f11db5b NeedsCompilation: no Package: mnem Version: 1.27.0 Depends: R (>= 4.1) 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: ef832e4696efa5b0dc2a64f0856793c6 NeedsCompilation: yes Package: mobileRNA Version: 1.7.1 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, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e6dc945f9dabb324ed7833c234736a9e NeedsCompilation: no Package: MODA Version: 1.37.0 Depends: R (>= 3.3) Imports: grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut, igraph, cluster, AMOUNTAIN, RColorBrewer Suggests: BiocStyle, knitr, rmarkdown License: GPL (>= 2) MD5sum: 08fa28f9be682fb93e311a8737137b0a NeedsCompilation: no Package: ModCon Version: 1.19.0 Depends: data.table, parallel, utils, stats, R (>= 4.1) Suggests: testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny, shinyFiles, shinydashboard, shinyjs License: GPL-3 + file LICENSE MD5sum: bb65e0569150df13ebc4d2947249e7f1 NeedsCompilation: no Package: Modstrings Version: 1.27.2 Depends: R 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utils, methods, terra, ggplot2, rlang, cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats Suggests: knitr, BiocStyle, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: b62c5fcf6eacfe0dabc40e2984f23504 NeedsCompilation: no Package: MOMA Version: 1.23.0 Depends: R (>= 4.0) Imports: circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics, grid, grDevices, magrittr, methods, MKmisc, MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr, reshape2, rlang, stats, stringr, tibble, tidyr, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, viper License: GPL-3 MD5sum: 32c3854c4c5e0697116eadc26ebd4659 NeedsCompilation: no Package: monaLisa Version: 1.17.1 Depends: R (>= 4.1) Imports: BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize, ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli, ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods, rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors, TFBSTools, tidyr, tools, utils, XVector Suggests: BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene License: GPL (>= 3) MD5sum: 69046971d1762e5e5741776731b0dd6f NeedsCompilation: no Package: monocle Version: 2.39.0 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: 4a2f500b5469e46f22203a7b18a64d3f NeedsCompilation: yes Package: MoonlightR Version: 1.37.0 Depends: R (>= 3.5), doParallel, foreach Imports: parmigene, randomForest, SummarizedExperiment, gplots, circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase, limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats, RISmed, grid, utils Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png, edgeR License: GPL (>= 3) MD5sum: 414d1a755d60de657cb21799ae882891 NeedsCompilation: no Package: mosaics Version: 2.49.0 Depends: R (>= 3.0.0), methods, graphics, Rcpp Imports: MASS, splines, lattice, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, Seqinfo, S4Vectors LinkingTo: Rcpp Suggests: mosaicsExample Enhances: parallel License: GPL (>= 2) MD5sum: 12ddf27c22dd6f3c9dd56d10e465ac81 NeedsCompilation: yes Package: MOSClip Version: 1.5.0 Depends: R (>= 4.4.0) Imports: MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix Suggests: RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) License: AGPL-3 MD5sum: c3a87e7f017413b17975566dc5be70b3 NeedsCompilation: no Package: mosdef Version: 1.7.0 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: a8926b5000130bee307356b73e93c241 NeedsCompilation: no Package: MOSim Version: 2.7.0 Depends: R (>= 4.2.0) Imports: HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2, lazyeval, matrixStats, methods, rlang, stringi, stringr, scran, Seurat, Signac, edgeR, Rcpp LinkingTo: cpp11, Rcpp Suggests: testthat, knitr, rmarkdown, codetools, BiocStyle, stats, utils, purrr, scales, tibble, tidyr, Biobase, scater, SingleCellExperiment, decor, markdown, Rsamtools, igraph, leiden, bluster License: GPL-3 MD5sum: e19d8ce511a09a09e1e477e9850eb92a NeedsCompilation: yes Package: Motif2Site Version: 1.15.0 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: d1b0c81315b0a7bc810ff76327412d41 NeedsCompilation: no Package: MotifDb Version: 1.53.0 Depends: R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges, Biostrings Imports: rtracklayer, splitstackshape Suggests: RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR, markdown License: Artistic-2.0 | file LICENSE License_is_FOSS: no License_restricts_use: yes MD5sum: 0081903c3fe6e73fdf944ed441bf5345 NeedsCompilation: no Package: motifmatchr Version: 1.33.0 Depends: R (>= 3.3) Imports: Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome, S4Vectors, SummarizedExperiment, GenomicRanges, IRanges, Rsamtools, Seqinfo LinkingTo: Rcpp, RcppArmadillo Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 + file LICENSE MD5sum: 7b66e29f258f2b10d83649b39d7006b7 NeedsCompilation: yes Package: MotifPeeker Version: 1.3.3 Depends: R (>= 4.6.0) Imports: BiocFileCache, BiocParallel, DT, ggplot2, plotly, universalmotif, GenomicRanges, IRanges, rtracklayer, tools, htmltools, rmarkdown, viridis, SummarizedExperiment, htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings, BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply, stats, utils Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39, downloadthis, knitr, markdown, methods, remotes, rworkflows, testthat (>= 3.0.0), withr, emoji, curl, jsonlite License: GPL (>= 3) MD5sum: 0fb96fb2ad2ec42616117905904e1c7a NeedsCompilation: no Package: motifStack Version: 1.55.0 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: a9fb4eb405c99c69f2cb24604be34060 NeedsCompilation: no Package: motifTestR Version: 1.7.0 Depends: Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0), Imports: Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats, methods, parallel, patchwork, rlang, S4Vectors, stats, universalmotif, Suggests: AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, extraChIPs (>= 1.13.3), ggdendro, knitr, MASS, MotifDb, rmarkdown, rtracklayer, SimpleUpset, testthat (>= 3.0.0), VGAM License: GPL-3 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downloadthis, DT, rmarkdown, BiocStyle License: MIT + file LICENSE MD5sum: 34a0efd270a01d1be3bd63134cc28560 NeedsCompilation: no Package: msPurity Version: 1.37.3 Depends: Rcpp Imports: plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW, stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite, BiocFileCache Suggests: MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA, RPostgres, RMySQL License: GPL-3 + file LICENSE MD5sum: 891615b3c0cea6a3bf9ebb205c67ae00 NeedsCompilation: no Package: msqrob2 Version: 1.19.2 Depends: R (>= 4.1), QFeatures (>= 1.1.2) Imports: stats, methods, lme4, purrr, BiocParallel, Matrix, MASS, limma, SummarizedExperiment, MultiAssayExperiment, codetools, matrixStats, ggplot2, assertthat, dplyr, grDevices, utils, rlang Suggests: stringr, ExploreModelMatrix, kableExtra, ComplexHeatmap, scater, multcomp, gridExtra, knitr, BiocStyle, RefManageR, sessioninfo, rmarkdown, testthat, tidyverse, tidyr, plotly, MsDataHub, MSnbase, MsCoreUtils, covr, arrow, data.table, ggcorrplot, iq License: Artistic-2.0 MD5sum: 37f6d7e020eef79d431904033a296344 NeedsCompilation: no Package: MsQuality Version: 1.11.3 Depends: R (>= 4.2.0) Imports: BiocParallel (>= 1.32.0), Chromatograms (>= 1.1.5), ggplot2 (>= 3.3.5), htmlwidgets (>= 1.5.3), methods (>= 4.2.0), MsDataHub (>= 1.10.0), MsExperiment (>= 0.99.0), plotly (>= 4.9.4.1), ProtGenerics (>= 1.24.0), rlang (>= 1.1.1), rmzqc (>= 0.7.0), shiny (>= 1.6.0), shinydashboard (>= 0.7.1), Spectra (>= 1.13.2), stats (>= 4.2.0), stringr (>= 1.4.0), tibble (>= 3.1.4), tidyr (>= 1.1.3), utils (>= 4.2.0), MsCoreUtils (>= 1.19.0), MetaboCoreUtils (>= 1.19.2) Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), dplyr (>= 1.0.5), knitr (>= 1.11), mzR (>= 2.32.0), rmarkdown (>= 2.7), S4Vectors (>= 0.29.17), testthat (>= 2.2.1) License: GPL-3 MD5sum: f7f67c34caf0aaf639597184709b04fc NeedsCompilation: no Package: MSstats Version: 4.19.2 Depends: R (>= 4.0) Imports: MSstatsConvert, data.table, 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Package: MultiDataSet Version: 1.39.0 Depends: R (>= 4.1), Biobase Imports: BiocGenerics, GenomicRanges, IRanges, S4Vectors, SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman, limma Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment License: file LICENSE MD5sum: 6a05b04a8bd6b3d7af51340e16c6c620 NeedsCompilation: no Package: multiGSEA Version: 1.21.0 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: 8237633a45a18a793342b3b56b34d9d7 NeedsCompilation: no Package: multiHiCcompare Version: 1.29.0 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: a1d0b5f53ce35ac2ef7ec2732544030a NeedsCompilation: no Package: MultiMed Version: 2.33.0 Depends: R (>= 3.1.0) Suggests: RUnit, BiocGenerics License: GPL (>= 2) + file LICENSE MD5sum: f201ed10f620547221d4a7690d21ae97 NeedsCompilation: no Package: MultimodalExperiment Version: 1.11.0 Depends: R (>= 4.3.0), IRanges, S4Vectors Imports: BiocGenerics, MultiAssayExperiment, methods, utils Suggests: BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 1c75afbc83a9e78c4956afbbc5f4445f NeedsCompilation: no Package: MultiRNAflow Version: 1.9.0 Depends: Mfuzz (>= 2.64.0), R (>= 4.4) Imports: Biobase (>= 2.54.0), ComplexHeatmap (>= 2.20.0), DESeq2 (>= 1.44.0), factoextra (>= 1.0.7), FactoMineR (>= 2.11), ggalluvial (>= 0.12.5), ggplot2 (>= 3.5.1), ggplotify (>= 0.1.2), ggrepel (>= 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389cb744d649f7bedfc2ea3674a734f9 NeedsCompilation: no Package: multiWGCNA Version: 1.9.3 Depends: R (>= 4.3.0), ggalluvial Imports: stringr, readr, WGCNA, magrittr, dplyr, reshape2, data.table, patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel, methods, SummarizedExperiment, ggraph, tidyr Suggests: BiocStyle, doParallel, ExperimentHub, knitr, markdown, rmarkdown, testthat (>= 3.0.0), vegan License: GPL-3 MD5sum: 3413c216c918d3a590697a5e513bad50 NeedsCompilation: no Package: multtest Version: 2.67.0 Depends: R (>= 2.10), methods, BiocGenerics, Biobase Imports: survival, MASS, stats4 Suggests: snow License: LGPL MD5sum: 9017c2039bfde3f4a6319a7ac39fd76a NeedsCompilation: yes Package: mumosa Version: 1.19.1 Depends: SingleCellExperiment Imports: stats, utils, methods, igraph, Matrix, BiocGenerics, BiocParallel, IRanges, S4Vectors, DelayedArray, DelayedMatrixStats, SummarizedExperiment, BiocNeighbors, BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran, batchelor, uwot Suggests: testthat, knitr, BiocStyle, rmarkdown, scater, bluster, DropletUtils, scRNAseq License: GPL-3 MD5sum: 5d62bf99066f4b6d2ab753d3ec1c6622 NeedsCompilation: no Package: MungeSumstats Version: 1.19.6 Depends: R(>= 4.1) Imports: data.table, utils, R.utils, dplyr, stats, GenomicRanges, GenomeInfoDb, IRanges, ieugwasr(>= 1.0.1), BSgenome, Biostrings, stringr, VariantAnnotation, methods, parallel, rtracklayer(>= 1.59.1), RCurl Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR, BiocStyle, covr, Rsamtools, MatrixGenerics, badger, BiocParallel, GenomicFiles License: Artistic-2.0 MD5sum: cf5b32b76d6392e15ceb02a81d022f70 NeedsCompilation: no Package: muscle Version: 3.53.0 Depends: Biostrings License: Unlimited MD5sum: 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d80becf90e0fdc3032c006d4ed04b6dd NeedsCompilation: no Package: MutationalPatterns Version: 3.21.1 Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6) Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>= 1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3), tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>= 1.8.8), IRanges (>= 2.6.0), Seqinfo, GenomeInfoDb (>= 1.45.9), Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>= 0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr, rmarkdown License: MIT + file LICENSE MD5sum: 27139d6ee0f82ddff86c4ddd06f4ad7e NeedsCompilation: no Package: mutscan Version: 1.1.1 Depends: R (>= 4.5.0) Imports: BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp, edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally, ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw, rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray, tools LinkingTo: Rcpp Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign, plotly, scattermore, BiocManager License: MIT + file LICENSE MD5sum: 307b02eea5ca769817bc277d12e54d2a NeedsCompilation: yes Package: MutSeqR Version: 0.99.9 Depends: R (>= 4.5.0) Imports: BiocGenerics, Biostrings, BSgenome, data.table, dplyr, GenomicRanges, ggplot2, here, IRanges, ggdendro, magrittr, methods, plyranges, rlang, S4Vectors, Seqinfo, stringr, SummarizedExperiment, tidyr, VariantAnnotation Suggests: binom, BiocManager, BiocStyle, bs4Dash, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, car, colorspace, dendsort, doBy, DT, ExperimentHub, fmsb, fs, ggrepel, gtools, htmltools, httr, knitr, lme4, magick, MutSeqRData, openxlsx, packcircles, patchwork, RColorBrewer, reticulate, rmarkdown, scales, shiny, testthat (>= 3.0.0), trackViewer, withr, yaml, xml2 License: MIT + file LICENSE MD5sum: 9782c7bbb21b5b3fb6abd5b883deb4a9 NeedsCompilation: no Package: MVCClass Version: 1.85.0 Depends: R (>= 2.1.0), methods License: LGPL MD5sum: 37f71c58cf5654f0d090d77a5ce28e44 NeedsCompilation: no Package: MWASTools Version: 1.35.0 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: 2d0be3050dfc68e9e0edd998698293e6 NeedsCompilation: no Package: myvariant Version: 1.41.0 Depends: R (>= 3.2.1), VariantAnnotation Imports: httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, Seqinfo, GenomeInfoDb Suggests: BiocStyle License: Artistic-2.0 MD5sum: 9175a27922f80c7143ccb31e45783280 NeedsCompilation: no Package: mzID 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parallel, GSA, limma, multtest, ICSNP, glmnet, network, ggplot2, grDevices, graphics, stats, utils Suggests: knitr, xtable, BiocStyle, testthat License: GPL-2 MD5sum: 15a63dac5eb5a7e65b35ce028c46aef5 NeedsCompilation: yes Package: NetPathMiner Version: 1.47.0 Depends: R (>= 3.0.2), igraph (>= 1.0) Suggests: rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: 2e947fdb75ed2273063567fd75b8d87d NeedsCompilation: yes Package: netresponse Version: 1.71.0 Depends: R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods, minet, mclust, reshape2 Imports: ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer Suggests: knitr License: GPL (>= 2) MD5sum: 55b42bdea70fd908a3a30fff46ed0d97 NeedsCompilation: yes Package: NetSAM Version: 1.51.0 Depends: R (>= 3.0.0), seriation (>= 1.0-6), igraph (>= 2.0.0), tools (>= 3.0.0), WGCNA (>= 1.34.0), biomaRt (>= 2.18.0) Imports: methods, AnnotationDbi (>= 1.28.0), doParallel (>= 1.0.10), foreach (>= 1.4.0), 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methods, MultiAssayExperiment, SummarizedExperiment, pracma, rlang, RSpectra, scales, stats Suggests: BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth, knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>= 4.0.0), spatstat.explore, stringr, survival, tidyverse, testthat (>= 3.0.0) License: GPL-3 MD5sum: 3b068f6b4f0bb1a8fdc9f4fc7583b062 NeedsCompilation: no Package: nnNorm Version: 2.75.0 Depends: R(>= 2.2.0), marray Imports: graphics, grDevices, marray, methods, nnet, stats License: LGPL MD5sum: 63e72a4909f24d4e396d1b332ab3e596 NeedsCompilation: no Package: nnSVG Version: 1.15.0 Depends: R (>= 4.2) Imports: SpatialExperiment, SingleCellExperiment, SummarizedExperiment, BRISC, BiocParallel, Matrix, matrixStats, stats, methods Suggests: BiocStyle, knitr, rmarkdown, STexampleData, WeberDivechaLCdata, scran, ggplot2, testthat License: MIT + file LICENSE MD5sum: 5cbd4cdce8cb3a7ebdcf2cd2ebd2f0a2 NeedsCompilation: no Package: NOISeq Version: 2.55.0 Depends: R (>= 2.13.0), methods, 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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, markdown License: MIT + file LICENSE MD5sum: 04afd580c560f8fd5780cd410f9ff601 NeedsCompilation: no Package: normalize450K Version: 1.39.0 Depends: R (>= 3.3), Biobase, illuminaio, quadprog Imports: utils License: BSD_2_clause + file LICENSE MD5sum: c55d7bf760b82208fbd1168b246f66cd NeedsCompilation: no Package: NormqPCR Version: 1.57.0 Depends: R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR, qpcR License: LGPL-3 MD5sum: 381843b573af5be4215b048da1443b36 NeedsCompilation: no Package: notame Version: 1.1.4 Depends: R (>= 4.5.0), ggplot2, SummarizedExperiment Imports: BiocGenerics, BiocParallel, dplyr, futile.logger, methods, openxlsx, S4Vectors, scales, stringr, tidyr, utils Suggests: BiocStyle, fpc, igraph, knitr, missForest, notameViz, notameStats, pcaMethods, RUVSeq, testthat License: MIT + file 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Biobase (>= 2.17.8), methods, graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7), SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>= 1.23.2), foreach, BiocManager, utils, S4Vectors (>= 0.9.25), RSQLite, DBI, ff Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, VanillaICE, crlmm Enhances: doMC, doMPI, doSNOW, doParallel, doRedis License: GPL (>= 2) MD5sum: 3bf4a071b70cdb24870302fae5bc9664 NeedsCompilation: no Package: OLIN Version: 1.89.0 Depends: R (>= 2.10), methods, locfit, marray Imports: graphics, grDevices, limma, marray, methods, stats Suggests: convert License: GPL-2 MD5sum: d5bb2bbe14fe372fb910cdcfa5b66371 NeedsCompilation: no Package: OLINgui Version: 1.85.0 Depends: R (>= 2.0.0), OLIN (>= 1.4.0) Imports: graphics, marray, OLIN, tcltk, tkWidgets, widgetTools License: 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rmarkdown, kableExtra, rtracklayer, IRanges, Seqinfo, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick Suggests: knitr, RUnit, BiocGenerics License: GPL-3 MD5sum: ecf3a5425a178c8c7c89167295a4b4f9 NeedsCompilation: no Package: omicsPrint Version: 1.31.0 Depends: R (>= 3.5), MASS Imports: methods, matrixStats, graphics, stats, SummarizedExperiment, MultiAssayExperiment, RaggedExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats License: GPL (>= 2) MD5sum: 7683c5ed9bff65d4535546e05b7628a1 NeedsCompilation: no Package: omicsViewer Version: 1.15.4 Depends: R (>= 4.2) Imports: htmltools, shinydashboard, survminer, survival, fastmatch, reshape2, stringr, beeswarm, grDevices, DT, shiny, shinythemes, shinyWidgets, plotly, networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea, openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics, grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2, S4Vectors, SummarizedExperiment, RSQLite, Matrix, shinycssloaders, ROCR, drc Suggests: BiocStyle, knitr, rmarkdown, unittest License: GPL-2 MD5sum: 2ce276d742e87de1d3ad3fe4fd28ac53 NeedsCompilation: no Package: Omixer Version: 1.21.0 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: 5c1ad77c5a86a3f285e7f2129b6ab989 NeedsCompilation: no Package: OmnipathR Version: 3.99.0 Depends: R(>= 4.0) Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), fs, httr2, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip 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Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz, ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>= 3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices LinkingTo: cpp11, BH(>= 1.62.0-1) Suggests: flowWorkspaceData, knitr, rmarkdown, markdown, testthat, utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2), MASS MD5sum: 4fc6a74eee3776765ba5b7ec31f1050e NeedsCompilation: yes Package: openPrimeR Version: 1.33.0 Depends: R (>= 4.0.0) Imports: Biostrings (>= 2.38.4), pwalign, XML (>= 3.98-1.4), scales (>= 0.4.0), reshape2 (>= 1.4.1), seqinr (>= 3.3-3), IRanges (>= 2.4.8), GenomicRanges (>= 1.22.4), ggplot2 (>= 2.1.0), plyr (>= 1.8.4), dplyr (>= 0.5.0), stringdist (>= 0.9.4.1), stringr (>= 1.0.0), RColorBrewer (>= 1.1-2), DECIPHER (>= 1.16.1), lpSolveAPI (>= 5.5.2.0-17), digest (>= 0.6.9), Hmisc (>= 3.17-4), ape (>= 3.5), BiocGenerics (>= 0.16.1), S4Vectors (>= 0.8.11), foreach (>= 1.4.3), magrittr (>= 1.5), uniqtag (>= 1.0), openxlsx (>= 4.0.17), grid (>= 3.1.0), 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Rfast, robustbase, dbscan, randomForest, foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse Suggests: knitr, BiocStyle, rmarkdown, magick License: Artistic-2.0 MD5sum: 205c65c86a793c418ecd576f65f50686 NeedsCompilation: no Package: OPWeight Version: 1.33.0 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: 0ae19c454786d48feeb4fc35f59eaba1 NeedsCompilation: no Package: OrderedList Version: 1.83.0 Depends: R (>= 3.6.1), Biobase, twilight Imports: methods License: GPL (>= 2) MD5sum: fc86af0b7487d42c99e953f7f0d873ca NeedsCompilation: no Package: ORFhunteR Version: 1.19.0 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 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scales, grDevices, graphics, stats, utils, methods Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown, BiocStyle License: GPL (>= 2) MD5sum: c597796bb23e0cebb8e0326065333411 NeedsCompilation: no Package: PICB Version: 1.3.0 Imports: utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods Suggests: GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 License: CC0 MD5sum: c03c3a1c66da37e3ff6dc2e97c172dd3 NeedsCompilation: no Package: pickgene Version: 1.83.0 Imports: graphics, grDevices, MASS, stats, utils License: GPL (>= 2) MD5sum: 243d4bf56a42de68cd03d3569df68287 NeedsCompilation: no Package: Pigengene Version: 1.37.0 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: 5aba40f44f9033257e0ee51c7d889312 NeedsCompilation: no Package: pipeComp Version: 1.21.0 Depends: R (>= 4.1) Imports: BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment, SummarizedExperiment, Seurat, matrixStats, Matrix, cluster, aricode, methods, utils, dplyr, grid, scales, scran, viridisLite, clue, randomcoloR, ggplot2, cowplot, intrinsicDimension, scater, knitr, reshape2, stats, Rtsne, uwot, circlize, RColorBrewer Suggests: BiocStyle, rmarkdown License: GPL MD5sum: 1cc1d12e7e1ee11683a8b58e8c5c84d7 NeedsCompilation: no Package: pipeFrame Version: 1.27.0 Depends: R (>= 4.0.0), Imports: BSgenome, digest, visNetwork, magrittr, methods, Biostrings, Seqinfo, parallel, stats, utils, rmarkdown Suggests: BiocManager, knitr, rtracklayer, testthat, BSgenome.Hsapiens.UCSC.hg19 License: GPL-3 MD5sum: dc9b884505cd5319d785e49a11ba39dc NeedsCompilation: no Package: PIPETS Version: 1.7.0 Depends: R (>= 4.4.0) Imports: dplyr, utils, stats, GenomicRanges, BiocGenerics, methods Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: d731f2c06a50755d3cba57858960f0ac NeedsCompilation: no Package: PIUMA Version: 1.7.2 Depends: R (>= 4.3) Imports: Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne, kernlab, vegan, dbscan, grDevices, stats, methods, SummarizedExperiment, ggplot2 Suggests: BiocStyle, testthat, knitr, rmarkdown, Seurat, SingleCellExperiment, aricode, mclust, viridis, magick, ggrepel, dplyr License: GPL-3 + file LICENSE MD5sum: 6b5ba8c38e9514e07ef4da42fd918440 NeedsCompilation: no Package: planet Version: 1.19.0 Depends: R (>= 4.3) Imports: methods, tibble, magrittr, dplyr Suggests: ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr, rmarkdown License: GPL-2 MD5sum: d52864af489845eae6594e781415408a NeedsCompilation: no Package: planttfhunter Version: 1.11.0 Depends: R (>= 4.2.0) Imports: Biostrings, SummarizedExperiment, utils, methods Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0) License: GPL-3 MD5sum: d82d80fabc304f0b795c0cf6728f75dd NeedsCompilation: no Package: plasmut Version: 1.9.0 Depends: R (>= 4.3.0) Imports: tibble, stats, dplyr Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf, BiocStyle, biocViews, testthat (>= 3.0.0) License: Artistic-2.0 MD5sum: f3bf2515fff99ce9985a61b88ec88919 NeedsCompilation: no Package: plgem Version: 1.83.0 Depends: R (>= 2.10) Imports: utils, Biobase (>= 2.5.5), MASS, methods License: GPL-2 MD5sum: a04c0abd5f9a8948598a97e37314e81c NeedsCompilation: no Package: plier Version: 1.81.0 Depends: R (>= 2.0), methods Imports: affy, Biobase, methods License: GPL (>= 2) MD5sum: 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SummarizedExperiment, TreeSummarizedExperiment, vegan, knitr, rmarkdown, BiocStyle, testthat, badger, pheatmap, Biobase License: GPL-3 MD5sum: 002ab0508742c735e82a7d1f2484f33a NeedsCompilation: no Package: plyinteractions Version: 1.9.3 Depends: R (>= 4.3.0), InteractionSet, plyranges Imports: Seqinfo, BiocGenerics, GenomicRanges, IRanges, S4Vectors, rlang, dplyr, tibble, tidyselect, methods, utils Suggests: tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings, BiocParallel, GenomeInfoDb, scales, HiContactsData, rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0), RefManageR License: Artistic-2.0 MD5sum: a96da57db5bb91b7be1fc9f1a027a281 NeedsCompilation: no Package: plyranges Version: 1.31.7 Depends: R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4), dplyr Imports: methods, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, Seqinfo, Rsamtools, S4Vectors (>= 0.23.10), utils Suggests: knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2 License: Artistic-2.0 MD5sum: f3835cf0b9b4914719baec5442609d22 NeedsCompilation: no Package: plyxp Version: 1.5.0 Depends: R (>= 4.5.0) Imports: dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect, vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods Suggests: devtools, knitr, rmarkdown, testthat, airway, IRanges, here License: MIT + file LICENSE MD5sum: a46cd509b9ce26ba8efb950a0d86160c NeedsCompilation: no Package: pmm Version: 1.43.0 Depends: R (>= 2.10) Imports: lme4, splines License: GPL-3 MD5sum: b6d2d3ea5908167390c459edef01a38d NeedsCompilation: no Package: pmp Version: 1.23.1 Depends: R (>= 4.0) Imports: stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick License: GPL-3 MD5sum: 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Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr License: GPL (>= 2) MD5sum: b8d99b41547009545e73945cd0763f55 NeedsCompilation: yes Package: poem Version: 1.3.0 Depends: R (>= 4.1.0) Imports: aricode, BiocNeighbors, BiocParallel, bluster, clevr, clue, cluster, elsa, fclust, igraph, Matrix, matrixStats, mclustcomp, methods, pdist, sp, spdep, stats, utils, SpatialExperiment, SummarizedExperiment Suggests: testthat (>= 3.0.0), BiocStyle, knitr, DT, dplyr, kableExtra, scico, cowplot, ggnetwork, ggplot2, tidyr, STexampleData License: GPL (>= 3) MD5sum: 3aca722190c45c419f45efae5d6e0874 NeedsCompilation: no Package: PolySTest Version: 1.5.3 Depends: R (>= 4.4.0) Imports: fdrtool (>= 1.2.15), limma (>= 3.61.3), matrixStats (>= 0.57.0), qvalue (>= 2.22.0), shiny (>= 1.5.0), SummarizedExperiment (>= 1.20.0), knitr (>= 1.33), plotly (>= 4.9.4), heatmaply (>= 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tidyr, utils, uwot, vegan Suggests: BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly, tidyverse, testthat (>= 2.3.2) License: GPL-3 MD5sum: 4ba59fe38af40f6c42e1120c5b4f6b5c NeedsCompilation: no Package: posDemux Version: 0.99.11 Depends: R (>= 4.6.0) Imports: Biostrings, ggplot2, methods, assertthat, glue, magrittr, dplyr, rlang, ShortRead, readr, shiny, purrr LinkingTo: Rcpp, Biostrings, IRanges, S4Vectors, XVector Suggests: testthat, devtools, DNABarcodes, knitr, rmarkdown, tibble, tidyr, BiocStyle, RefManageR, sessioninfo, DBI, chunked, RSQLite, dbplyr License: AGPL (>= 3) MD5sum: d7205291acb6c70a2c8bd813606e79ba NeedsCompilation: yes Package: postNet Version: 0.99.8 Depends: R (>= 4.5.0), Imports: dplyr, plyr, Biostrings, data.table, gridExtra, seqinr, R.utils, reshape2, vioplot, stringr, plotrix, gplots, ggplot2, ggrepel, anota2seq, memes, GenomicRanges, IRanges, WriteXLS, randomForest, igraph, Boruta, ROCR, caret, msigdb, ExperimentHub, AnnotationHub, GSEABase, fgsea, org.Hs.eg.db, org.Mm.eg.db, RColorBrewer, httr2, rvest, umap, clusterProfiler (>= 4.18.4), gage, withr, grDevices, graphics, methods, stats, utils, tools, BiocFileCache, curl LinkingTo: Rcpp, BH Suggests: knitr, rmarkdown, BiocStyle, pdftools, magick, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: e880ca2b6c4e70eba2813c7c8f2ba643 NeedsCompilation: yes Package: powerTCR Version: 1.31.0 Imports: cubature, doParallel, evmix, foreach, magrittr, methods, parallel, purrr, stats, truncdist, vegan, VGAM Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics License: Artistic-2.0 MD5sum: 234626b49376017964dd649475ff00f1 NeedsCompilation: no Package: POWSC Version: 1.19.0 Depends: R (>= 4.1), Biobase, SingleCellExperiment, MAST Imports: pheatmap, ggplot2, RColorBrewer, grDevices, SummarizedExperiment, limma Suggests: rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle License: GPL-2 MD5sum: 5151ea18278671cabc35222fb2beed6b NeedsCompilation: no Package: ppcseq Version: 1.19.0 Depends: R (>= 4.1.0), rstan (>= 2.18.1) Imports: benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics, lifecycle, magrittr, methods, parallel, purrr, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1), stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) Suggests: knitr, testthat, BiocStyle, rmarkdown License: GPL-3 MD5sum: ceea87663fba66c1ca8104c6a369e20c NeedsCompilation: yes Package: PPInfer Version: 1.37.0 Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData Imports: httr, grDevices, graphics, stats, utils License: Artistic-2.0 MD5sum: f2fc8d02e41d948467a6e950668a3417 NeedsCompilation: no Package: pqsfinder Version: 2.27.0 Depends: R (>= 3.5.0), Biostrings Imports: Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods LinkingTo: Rcpp, BH (>= 1.78.0) Suggests: BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi License: BSD_2_clause + file LICENSE MD5sum: 3cd07f774e78d96cd9edca415e74ae70 NeedsCompilation: yes Package: pram Version: 1.27.0 Depends: R (>= 3.6) Imports: methods, BiocParallel, tools, utils, data.table (>= 1.11.8), GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6), BiocGenerics (>= 0.26.0), Seqinfo, GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>= 1.32.3), S4Vectors (>= 0.18.3) Suggests: testthat, BiocStyle, knitr, rmarkdown License: GPL (>= 3) MD5sum: d8e1d488111b644aa1d5e9cfc18a9c31 NeedsCompilation: no Package: prebs Version: 1.51.0 Depends: R (>= 2.14.0), GenomicAlignments, affy, RPA Imports: parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, Seqinfo, S4Vectors Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe License: Artistic-2.0 MD5sum: 7fd39955c418d437bab3ef8671f65f0c NeedsCompilation: no Package: preciseTAD Version: 1.21.0 Depends: R (>= 4.1) Imports: 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e1071, parallel, foreach, doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR, robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors LinkingTo: Rcpp, RcppArmadillo Suggests: knitr, rmarkdown, mclust, scater, BiocStyle License: GPL-3 MD5sum: 288e9cde769d8ecbe205ee7494ceec9f NeedsCompilation: yes Package: Scale4C Version: 1.33.0 Depends: R (>= 3.5.0), smoothie, GenomicRanges, IRanges, SummarizedExperiment Imports: methods, grDevices, graphics, utils License: LGPL-3 MD5sum: 18fae32a78449dcd5a302d8e249380d7 NeedsCompilation: no Package: ScaledMatrix Version: 1.19.0 Imports: methods, Matrix, S4Vectors, DelayedArray Suggests: testthat, BiocStyle, knitr, rmarkdown, BiocSingular, DelayedMatrixStats License: GPL-3 MD5sum: 69729298f86ae4772a2387921cb49147 NeedsCompilation: no Package: SCAN.UPC Version: 2.53.0 Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva Imports: 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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: 97d61c55a9c4fd896c075996c0793ece NeedsCompilation: yes Package: scGraphVerse Version: 1.1.0 Depends: R (>= 4.5.0) Imports: BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG, GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, distributions3, dplyr, grDevices, graphics, httr, igraph, jsonlite, methods, parallel, reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors, graph, mpath Suggests: AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot, fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db, org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA, rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0), knitr, rmarkdown, tidyverse, magick, celldex, SingleR, TENxPBMCData, scater, GenomeInfoDb, GenomicRanges, License: GPL-3 + file LICENSE MD5sum: 0b57e179232e4ba5d13eed2a99aa31d3 NeedsCompilation: yes Package: schex Version: 1.25.0 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: 1c46a4bc51bd3b215d9d5b7f14cb801f NeedsCompilation: no Package: scHiCcompare Version: 1.3.0 Depends: R (>= 4.5.0) Imports: grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel Suggests: knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra License: MIT + file LICENSE MD5sum: ba1d78a64bc23fd27c6419ba0da6aca5 NeedsCompilation: no Package: scHOT Version: 1.23.0 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: 89bfc5f3e7278905d9aaa0c79d951fac NeedsCompilation: no Package: scider Version: 1.9.0 Depends: R (>= 4.3) Imports: SpatialExperiment, SummarizedExperiment, spatstat.geom, spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats, pheatmap, plotly, shiny, igraph, janitor, knitr, methods, utils, isoband, S4Vectors, grDevices, dbscan, hexDensity, hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba Suggests: edgeR, testthat (>= 3.0.0) License: GPL-3 + file LICENSE MD5sum: 6bb39dedac38d295820426fbd516a13a NeedsCompilation: yes Package: scLANE Version: 1.1.3 Depends: glm2, magrittr, R (>= 4.5.0) Imports: geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr, furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2, splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr, tidyselect, broom.mixed, Rcpp LinkingTo: Rcpp, RcppEigen Suggests: covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba, rlang, magick, igraph, scater, gtable, ggpubr, viridis, bluster, cluster, circlize, speedglm, rmarkdown, gridExtra, BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel, BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0), testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment License: MIT + file LICENSE MD5sum: 3c94004ed205f34479bbed2052aea9fb NeedsCompilation: yes Package: scLang Version: 0.99.3 Imports: dplyr, ggplot2, henna, methods, paletteer, rlang, S4Vectors, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment Suggests: BiocStyle, knitr, qs2, rmarkdown, scater, scRNAseq, Seurat, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 306dadf4241f003d395a5f0c64ed2ae7 NeedsCompilation: no Package: scmap Version: 1.33.0 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: 47ff92b0388559864ce30554e269e09b NeedsCompilation: yes Package: scMerge Version: 1.27.0 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: c1714101c300f20ac2640fa15c3db355 NeedsCompilation: no Package: scMET Version: 1.13.0 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: d8433096ad549ef0d67ee17deab54299 NeedsCompilation: yes Package: scMultiSim Version: 1.7.0 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: 3e6b8ff41387414de096ff0756b4404f NeedsCompilation: no Package: SCnorm Version: 1.33.0 Depends: R (>= 3.4.0), Imports: SingleCellExperiment, SummarizedExperiment, stats, methods, graphics, grDevices, parallel, quantreg, cluster, moments, data.table, BiocParallel, S4Vectors, ggplot2, forcats, BiocGenerics Suggests: BiocStyle, knitr, rmarkdown, devtools License: GPL (>= 2) MD5sum: 65a5ae54b1a0862f29428b6f0046911b NeedsCompilation: no Package: scone Version: 1.35.0 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, SparseArray (>= 1.7.6) Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray, visNetwork, doParallel, batchtools, splatter, scater, kableExtra, mclust, TENxPBMCData License: Artistic-2.0 MD5sum: 0124fd6ee4bee35d24145cd6e63bef59 NeedsCompilation: no Package: Sconify Version: 1.31.0 Depends: R (>= 3.5) Imports: tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils, stats, readr Suggests: knitr, rmarkdown, testthat License: Artistic-2.0 MD5sum: 58404b0e6dca99f2c54fb9f98d0e57ae NeedsCompilation: no Package: SCOPE Version: 1.23.0 Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb, BSgenome.Hsapiens.UCSC.hg19 Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer, gplots, foreach, parallel, doParallel, DNAcopy, BSgenome, Biostrings, BiocGenerics, S4Vectors Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) License: GPL-2 MD5sum: 58bdb6d06c26830afb27dfbe8c8e9af1 NeedsCompilation: no Package: scoreInvHap Version: 1.33.0 Depends: R (>= 3.6.0) Imports: Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment Suggests: testthat, knitr, BiocStyle, rmarkdown License: file LICENSE MD5sum: 68b46f74a40693f91c6dccc244fea013 NeedsCompilation: no Package: scoup Version: 1.5.5 Depends: R (>= 4.4), Matrix Imports: Biostrings, methods Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml License: GPL (>= 2) MD5sum: a2ea660a4b8332de111d641efcf8230f NeedsCompilation: no Package: scp Version: 1.21.1 Depends: R (>= 4.3.0), QFeatures (>= 1.19.1) 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: 2d32b9f4845cb4e9c56b51d7babdeb7a NeedsCompilation: no Package: scPassport Version: 0.99.2 Depends: R (>= 4.3) Imports: shiny, miniUI, Rcpp, S4Vectors LinkingTo: Rcpp Suggests: Seurat, SingleCellExperiment, SummarizedExperiment, knitr, rmarkdown, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: a69f95a29ea3deebb1b499d88833a852 NeedsCompilation: yes Package: scPCA Version: 1.25.0 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: d15e9b7de3a76b1eaeca018ebc2ce524 NeedsCompilation: no Package: scran Version: 1.39.2 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, scrapper License: GPL-3 MD5sum: ab324550da5cee3919f63f69dede4bea NeedsCompilation: yes Package: scrapper Version: 1.5.18 Imports: methods, Rcpp, beachmat (>= 2.25.1), S4Vectors, SparseArray, DelayedArray, BiocNeighbors (>= 1.99.0), parallel LinkingTo: Rcpp, assorthead (>= 1.5.16), beachmat, BiocNeighbors, Rigraphlib Suggests: testthat, knitr, rmarkdown, BiocStyle, Matrix, IRanges, SummarizedExperiment, SingleCellExperiment, scRNAseq, org.Mm.eg.db, scater, igraph License: MIT + file LICENSE MD5sum: e6e84e8a2a94ac38cb29d085815e8780 NeedsCompilation: yes Package: scReClassify Version: 1.17.0 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: 3a62b8af64409a569fae80e1f5295855 NeedsCompilation: no Package: scRecover Version: 1.27.0 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: 0f404a9ef7b484193c8f055b18c9e0bb NeedsCompilation: no Package: screenCounter Version: 1.11.0 Depends: S4Vectors, SummarizedExperiment Imports: Rcpp, BiocParallel LinkingTo: Rcpp Suggests: BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown, testthat License: MIT + file LICENSE MD5sum: 089d0d244f26fa9380cd576add3d4860 NeedsCompilation: yes Package: ScreenR Version: 1.13.1 Depends: R (>= 4.3) Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>= 3.46), patchwork (>= 1.1), tibble (>= 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circlize, ComplexHeatmap, colourpicker, data.table, desc, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro, ggforce, ggnewscale, ggplot2, ggrepel, ggridges, grDevices, grid, gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr, methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2, 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, shinytest2 Enhances: celldex, future, SingleR, SummarizedExperiment, tricycle, terra License: GPL-3 MD5sum: 1622ed6cfcaeb0a97bca1029866c7979 NeedsCompilation: no Package: scry Version: 1.23.0 Depends: R (>= 4.0), stats, methods Imports: DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment, SummarizedExperiment, BiocSingular Suggests: BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array, knitr, markdown, rmarkdown, TENxPBMCData, testthat License: Artistic-2.0 MD5sum: 9d5f4836cf7a4b31ea57efc74edd91f2 NeedsCompilation: no Package: scShapes Version: 1.17.0 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: 0019ba4f81f2b49dc0259f59fa6bfcc4 NeedsCompilation: yes Package: scTGIF Version: 1.25.0 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: e6072ec5dd73a1d8b67570601e4d0b6f NeedsCompilation: no Package: scTHI Version: 1.23.0 Depends: R (>= 4.0) Imports: BiocParallel, Rtsne, grDevices, graphics, stats Suggests: scTHI.data, knitr, rmarkdown, BiocStyle License: GPL-2 MD5sum: e0e8c34aeb05cb41c2e7831082c7b6ee NeedsCompilation: no Package: scToppR Version: 0.99.10 Depends: R (>= 4.5.0) Imports: dplyr, forcats, ggplot2, stringr, openxlsx, viridis, patchwork, utils, httr2 Suggests: airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors, SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0) License: MIT + file LICENSE MD5sum: 818c453ce70d5574b0721a922b97ed3f NeedsCompilation: no Package: scTreeViz Version: 1.17.0 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: 1c5886d0623c6c7d7ea984521ed443c5 NeedsCompilation: no Package: scTypeEval Version: 0.99.31 Depends: R (>= 4.6.0) Imports: Matrix (>= 1.6-5), BiocParallel (>= 1.34.2), dplyr (>= 1.1.4), tidyr (>= 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NeedsCompilation: no Package: Seqinfo Version: 1.1.0 Depends: methods, BiocGenerics Imports: stats, S4Vectors (>= 0.47.6), IRanges Suggests: GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 0d9c553c3274573d1b92a33474945765 NeedsCompilation: no Package: seqLogo Version: 1.77.0 Depends: R (>= 4.2), methods, grid Imports: stats4, grDevices Suggests: knitr, BiocStyle, rmarkdown, testthat License: LGPL (>= 2) MD5sum: fe2f96cf23cbdcd7ab6eb25d11451fcb NeedsCompilation: no Package: seqPattern Version: 1.43.0 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: 7e14a2f06152a5578a3d351d096a6315 NeedsCompilation: no Package: seqsetvis 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RSpectra, zeallot LinkingTo: Rcpp, RcppArmadillo Suggests: BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS, patchwork, rmarkdown, scater, scuttle, SingleCellExperiment, sparseMatrixStats, stringr, TENxPBMCData, testthat (>= 3.0.0), tibble License: MIT + file LICENSE MD5sum: 6a120033562c3adb6f73d211e1eb0f9f NeedsCompilation: yes Package: SeqVarTools Version: 1.49.0 Depends: SeqArray Imports: grDevices, graphics, stats, methods, Biobase, BiocGenerics, gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf, Matrix, data.table, Suggests: BiocStyle, RUnit, stringr License: GPL-3 MD5sum: 88029290398f24d632dd4ecffb2fd34e NeedsCompilation: no Package: SEraster Version: 1.3.0 Depends: R (>= 4.5.0) Imports: BiocParallel, ggplot2, Matrix, methods, rearrr, sf, SpatialExperiment, SummarizedExperiment Suggests: CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr, rmarkdown, BiocManager, remotes License: GPL-3 MD5sum: a962f56c0f23717f69b16416978488b5 NeedsCompilation: no 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stats4, grDevices, graphics, stats, scrime (>= 1.2.5) Suggests: affy, annotate, genefilter, KernSmooth License: LGPL (>= 2) MD5sum: 99762cb34e56e86f9e88afc8dc6ad461 NeedsCompilation: no Package: sights Version: 1.37.0 Depends: R(>= 3.3) Imports: MASS(>= 7.3), qvalue(>= 2.2), ggplot2(>= 2.0), reshape2(>= 1.4), lattice(>= 0.2), stats(>= 3.3) Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx License: GPL-3 | file LICENSE MD5sum: 09c8cac864c02d782885831be824f481 NeedsCompilation: no Package: signeR Version: 2.13.0 Depends: R (>= 4.1.0), NMF Imports: BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats, utils, PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat, future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada, future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv, reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble, readr, shiny, shinydashboard, shinycssloaders, shinyWidgets, bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer, BSgenome, broom, VariantAnnotation LinkingTo: Rcpp, RcppArmadillo (>= 0.7.100) Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, rmarkdown License: GPL-3 MD5sum: a914dc85c381fcf3737b2b4be70d4af1 NeedsCompilation: yes Package: SigsPack Version: 1.25.0 Depends: R (>= 3.6) Imports: quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0), VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb, GenomicRanges, rtracklayer, SummarizedExperiment, graphics, stats, utils Suggests: IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, rmarkdown License: GPL-3 MD5sum: c72d84e0da6d3e55933c8bc92883a124 NeedsCompilation: no Package: sigsquared Version: 1.43.0 Depends: R (>= 3.2.0), methods Imports: Biobase, survival Suggests: RUnit, BiocGenerics License: GPL-3 MD5sum: c30b564d800e2e86996633cd7136a010 NeedsCompilation: no Package: SIM Version: 1.81.0 Depends: R (>= 3.5), quantreg Imports: graphics, stats, globaltest, 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(>= 4.5.0), SingleCellExperiment Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick License: GPL-3 MD5sum: 1eff204bfe85224cc161ca954452cb40 NeedsCompilation: no Package: simplifyEnrichment Version: 2.5.1 Depends: R (>= 4.1.0) 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: 70c4da6354a8686383c61444155b5611 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BiocStyle, ExperimentHub, lme4, lmerTest, ggfortify, tidyr, testthat (>= 3.0.0) License: GPL (>= 3) + file LICENSE MD5sum: b133cee72bc783fdc4e0f7a4df5e006c NeedsCompilation: no Package: SpaceMarkers Version: 2.1.0 Depends: R (>= 4.4.0) Imports: matrixStats, matrixTests, rstatix, spatstat.explore, spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix, qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer, circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis Suggests: data.table, devtools, knitr, cowplot, rjson, rmarkdown, BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap Enhances: BiocParallel License: MIT + file LICENSE MD5sum: adcbf6b5142dfca880892a94e1d84daf NeedsCompilation: no Package: spacexr Version: 1.3.0 Depends: R (>= 4.5.0) Imports: ggplot2, Matrix, parallel, quadprog, httr, methods, memoise, BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie, SpatialExperiment Suggests: BiocStyle, knitr, rmarkdown, testthat License: GPL (>= 3) MD5sum: 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rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>= 3.0.0) License: CC BY 4.0 MD5sum: bbbcd6cb33dd6e40d89e1d230e162a35 NeedsCompilation: no Package: tidySingleCellExperiment Version: 1.21.0 Depends: R (>= 4.4.0), SingleCellExperiment, ttservice (>= 0.4.0) Imports: dplyr, tidyr, SummarizedExperiment, tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi, Matrix, stats Suggests: BiocStyle, testthat, knitr, markdown, rmarkdown, SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph, GGally, uwot, celldex, dittoSeq, plotly, rbibutils, prettydoc License: GPL-3 MD5sum: 476b5f9d062923f6a6eaf675aa1ffc9d NeedsCompilation: no Package: tidySpatialExperiment Version: 1.7.2 Depends: R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment, ttservice Imports: SummarizedExperiment, SingleCellExperiment, BiocGenerics, S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr, ggplot2 (>= 4.0.0), 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puma, lumi, BiocStyle, BiocManager License: AGPL-3 MD5sum: ee17f175e45d55132647335799a19ac8 NeedsCompilation: yes Package: TileDBArray Version: 1.21.2 Depends: SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7) Imports: methods, tiledb, S4Vectors Suggests: knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat License: MIT + file LICENSE MD5sum: 8d329a25bb9ae2312a9b681093773cee NeedsCompilation: no Package: tilingArray Version: 1.89.0 Depends: R (>= 2.11.0), Biobase, methods, pixmap Imports: strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4 License: Artistic-2.0 MD5sum: c9f35ed67954d7e72d1c927dbdacd407 NeedsCompilation: yes Package: timecourse Version: 1.83.0 Depends: R (>= 2.1.1), MASS, methods Imports: Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods, stats License: LGPL MD5sum: 0ef71b9acdffc822b175a07fe7eefaba NeedsCompilation: no Package: timeOmics Version: 1.23.0 Depends: mixOmics, R (>= 4.0) Imports: dplyr, tidyr, tibble, purrr, magrittr, ggplot2, 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htmlwidgets, jsonlite, data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat License: AGPL-3 MD5sum: d0b2e11b70eff4be5825ee6d8a9a89bc NeedsCompilation: no Package: TOAST Version: 1.25.0 Depends: R (>= 3.6), EpiDISH, limma, nnls, quadprog Imports: stats, methods, SummarizedExperiment, corpcor, doParallel, parallel, ggplot2, tidyr, GGally Suggests: BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix License: GPL-2 MD5sum: 55f7932b366c315b621761680a9fb18e NeedsCompilation: no Package: tomoda Version: 1.21.0 Depends: R (>= 4.0.0) Imports: methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment Suggests: knitr, rmarkdown, BiocStyle, testthat License: MIT + file LICENSE MD5sum: f62bf76223aeacaa4536daecbaa7d31b NeedsCompilation: no Package: tomoseqr Version: 1.15.0 Depends: R (>= 4.2) Imports: grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, 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rtracklayer, S4Vectors, stats, utils Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat, e1071 License: GPL-3 MD5sum: 8bced0fa8344031c726995da414fbff2 NeedsCompilation: no Package: transite Version: 1.29.0 Depends: R (>= 3.5) Imports: BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>= 0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0), grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>= 1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), stringr (>= 1.5.1), utils LinkingTo: Rcpp (>= 1.0.4.8) Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0), testthat (>= 2.1.0) License: MIT + file LICENSE MD5sum: e829f88f4b3da8ec0e27cccbbdc7b28b NeedsCompilation: yes Package: tRanslatome Version: 1.49.0 Depends: R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix, Biobase License: GPL-3 MD5sum: d038918b62f63bd5b345e4dbff13f1f7 NeedsCompilation: no Package: 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stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector, Biostrings, Modstrings, ggplot2, scales Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport License: GPL-3 + file LICENSE MD5sum: b7d814541ce57e6aa8d59dd6390b25c6 NeedsCompilation: no Package: tRNAdbImport Version: 1.29.0 Depends: R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA Imports: Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges, utils Suggests: BiocGenerics, knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer License: GPL-3 + file LICENSE MD5sum: e72db643724a63459248a28b3a11b244 NeedsCompilation: no Package: tRNAscanImport Version: 1.31.0 Depends: R (>= 3.5), GenomicRanges, tRNA Imports: methods, stringr, BiocGenerics, Biostrings, Structstrings, S4Vectors, IRanges, XVector, Seqinfo, rtracklayer, BSgenome, Rsamtools Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2, BSgenome.Scerevisiae.UCSC.sacCer3 License: GPL-3 + file LICENSE MD5sum: c370d7f1d27ad850f8931b2db8fd0b74 NeedsCompilation: no Package: TRONCO Version: 2.43.1 Depends: R (>= 4.1.0), Imports: bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel, iterators, RColorBrewer, circlize, igraph, grid, gridExtra, xtable, gtable, scales, R.matlab, grDevices, graphics, stats, utils, methods Suggests: BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways, magick License: GPL-3 MD5sum: 393262b2434aa4d680e214c20709c992 NeedsCompilation: no Package: TSAR Version: 1.9.3 Depends: R (>= 4.3.0) Imports: dplyr (>= 1.0.7), ggplot2 (>= 3.3.5), ggpubr (>= 0.4.0), magrittr (>= 2.0.3), mgcv (>= 1.8.38), readxl (>= 1.4.0), stringr (>= 1.4.0), tidyr (>= 1.1.4), utils (>= 4.3.1), shiny (>= 1.7.4.1), plotly (>= 4.10.2), shinyjs (>= 2.1.0), jsonlite (>= 1.8.7), rhandsontable (>= 0.3.8), openxlsx (>= 4.2.5.2), shinyWidgets (>= 0.7.6), minpack.lm (>= 1.2.3) Suggests: knitr, rmarkdown, testthat (>= 3.0.0) License: AGPL-3 MD5sum: 370f90615d794c09f474cf91485e3b95 NeedsCompilation: no Package: TSCAN Version: 1.49.0 Depends: R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils Imports: ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv, mclust, gplots, methods, stats, Matrix, SummarizedExperiment, SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors Suggests: knitr, testthat, scuttle, scran, metapod, BiocParallel, BiocNeighbors, batchelor License: GPL (>= 2) MD5sum: 4a01b6a2c38e713e721a7a355cccbec0 NeedsCompilation: no Package: ttgsea Version: 1.19.0 Depends: keras Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats Suggests: fgsea, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: dca63e6ddda6bb5a56716065e156412e NeedsCompilation: no Package: TTMap Version: 1.33.0 Depends: rgl, colorRamps Imports: grDevices,graphics,stats,utils, methods, SummarizedExperiment, Biobase Suggests: BiocStyle, airway License: GPL-2 MD5sum: e375a02b50d2dd9d39514f4cc6c9fc49 NeedsCompilation: no Package: TurboNorm Version: 1.59.0 Depends: R (>= 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License: GPL (>= 2) MD5sum: 4838e472a0ee9e42749ff5db3d718aa2 NeedsCompilation: yes Package: twilight Version: 1.87.0 Depends: R (>= 2.10) Imports: Biobase, graphics, grDevices, splines, stats Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) License: GPL (>= 2) MD5sum: b11468cabb77a83aa28e848a938d5a6b NeedsCompilation: yes Package: twoddpcr Version: 1.35.1 Depends: R (>= 3.4) Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle License: GPL-3 MD5sum: 6af45918ef75fcc3e6f9f0fc23e557b0 NeedsCompilation: no Package: tximport Version: 1.39.2 Imports: utils, stats, methods Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow, limma, edgeR (>= 4.9.2), DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix, eds License: LGPL (>= 2) MD5sum: 13d3d0bd676b3a07412cd698495c80d0 NeedsCompilation: no Package: UCell Version: 2.15.1 Depends: R(>= 4.3.0) Imports: methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel, BiocNeighbors, SingleCellExperiment, SummarizedExperiment Suggests: scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle, Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown License: GPL-3 + file LICENSE MD5sum: ee4111e1afa5aaff7bf5094e547a9647 NeedsCompilation: no Package: UCSC.utils Version: 1.7.1 Imports: methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6) Suggests: DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: e64e96c4ec4feb2bdd41bc4eca78080d NeedsCompilation: no Package: UMI4Cats Version: 1.21.0 Depends: R (>= 4.1.0), SummarizedExperiment Imports: magick, cowplot, scales, GenomicRanges, ShortRead, zoo, ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments, RColorBrewer, utils, grDevices, stats, annotate, rlang, GenomicFeatures, BiocFileCache, rappdirs, fda, BiocGenerics Suggests: knitr, rmarkdown, BiocStyle, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, tidyr, testthat License: Artistic-2.0 MD5sum: ab6ab953ba826e39c9554969dca61308 NeedsCompilation: no Package: uncoverappLib Version: 1.21.0 Imports: markdown, shiny, shinyjs, shinyBS, shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx, condformat, stringr, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs, TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,S4Vectors, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx, Rsamtools, GenomicRanges Suggests: BiocStyle, knitr, testthat, rmarkdown, dplyr License: MIT + file LICENSE MD5sum: 5329417cc7047aa28f45770db23c28e8 NeedsCompilation: no Package: UNDO Version: 1.53.0 Depends: R (>= 2.15.2), methods, BiocGenerics, Biobase Imports: MASS, boot, nnls, stats, utils License: GPL-2 MD5sum: 1e83748520d0a42a2c18f1939de3bb77 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rlang, grid, MatrixGenerics LinkingTo: Rcpp, RcppThread Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb, testthat, BiocParallel, seqLogo, motifStack, dplyr, ape, ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio Enhances: PWMEnrich, rGADEM License: GPL-3 MD5sum: 3ba256276e8b8464a7a4a2859c7ec12c NeedsCompilation: yes Package: updateObject Version: 1.15.0 Depends: R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors Imports: utils, digest Suggests: GenomicRanges, SummarizedExperiment, InteractionSet, SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat, knitr, rmarkdown, BiocStyle License: Artistic-2.0 MD5sum: 069ade1347d6cb9ce0398cb1a4fb5bea NeedsCompilation: no Package: uSORT Version: 1.37.0 Depends: R (>= 3.3.0), tcltk Imports: igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr, methods, cluster, Biobase, fpc, BiocGenerics, monocle, grDevices, graphics, stats, utils Suggests: knitr, RUnit, testthat, ggplot2 License: Artistic-2.0 MD5sum: 2f60b919f60ad908ad3e11963e31e7bd NeedsCompilation: no Package: VAExprs Version: 1.17.0 Depends: keras, mclust Imports: SingleCellExperiment, SummarizedExperiment, tensorflow, scater, CatEncoders, DeepPINCS, purrr, DiagrammeR, stats Suggests: SC3, knitr, testthat, reticulate, rmarkdown License: Artistic-2.0 MD5sum: 34244d9bb07695481fb61f6c824b8007 NeedsCompilation: no Package: VanillaICE Version: 1.73.0 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: 43cb7d4f99543aa33afdca28c238f4eb NeedsCompilation: yes Package: VarCon Version: 1.19.0 Depends: Biostrings, BSgenome, GenomicRanges, R (>= 4.1) Imports: methods, stats, IRanges, shiny, shinycssloaders, shinyFiles, ggplot2 Suggests: testthat, knitr, rmarkdown License: GPL-3 MD5sum: f2e17d34541a904147354ec5e81193af NeedsCompilation: no Package: VariantAnnotation Version: 1.57.1 Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1) Imports: utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2), AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome (>= 1.77.1), GenomicFeatures (>= 1.61.4), curl LinkingTo: S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0) Suggests: GenomeInfoDb, 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: a623d17425448738492831cead7dc085 NeedsCompilation: yes Package: VariantExperiment Version: 1.25.0 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: 53c6c22869bbe89898add2d6d8567665 NeedsCompilation: no Package: VariantTools Version: 1.53.2 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, 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knitr License: file LICENSE MD5sum: 4810e322d328f5b7cb579a2a911caa8d NeedsCompilation: no Package: vidger Version: 1.31.0 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: 86d3e1e73423df94585b411a7bddb061 NeedsCompilation: no Package: viper Version: 1.45.0 Depends: R (>= 2.14.0), Biobase, methods Imports: mixtools, stats, parallel, e1071, KernSmooth Suggests: bcellViper License: file LICENSE MD5sum: d49a8d6649c360a4eea4fcb602b11015 NeedsCompilation: no Package: ViSEAGO Version: 1.25.0 Depends: R (>= 3.6) Imports: data.table, AnnotationDbi, dendextend, dynamicTreeCut, GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT, DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea, ggplot2, htmlwidgets, igraph, methods, plotly, scales, ComplexHeatmap, circlize Suggests: htmltools, org.Mm.eg.db, limma, Rgraphviz, 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ggridges, ggalluvial, ggcorrplot, ggrain, ggvenn, enrichplot, knitr, magrittr, patchwork, org.Hs.eg.db, org.Mm.eg.db, quarto, rmarkdown, yaml, writexl, testthat (>= 3.0.0), uwot, xCell2 License: GPL-3 MD5sum: 1f8aa7b6bdc746c939fffdd4ae1dc523 NeedsCompilation: no Package: VplotR Version: 1.21.0 Depends: R (>= 4.0), GenomicRanges, IRanges, ggplot2 Imports: cowplot, magrittr, Seqinfo, 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: c56dba4792d7f59fd6bdcff42901a838 NeedsCompilation: no Package: vsclust Version: 1.13.1 Depends: R (>= 4.2.0) Imports: matrixStats, limma, parallel, shiny, qvalue, grDevices, stats, MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics LinkingTo: Rcpp Suggests: knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr, magick License: GPL-2 MD5sum: 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Depends: R (>= 2.4.0), methods, utils, tcltk Suggests: Biobase License: LGPL MD5sum: 617581be46db1a1aa071c428685e5aee NeedsCompilation: no Package: wiggleplotr Version: 1.35.2 Depends: R (>= 3.6) Imports: dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer, cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter, arrow License: Apache License 2.0 MD5sum: 77464048ecf26e4162a31848eb28287f NeedsCompilation: no Package: wpm Version: 1.21.0 Depends: R (>= 4.1.0) Imports: utils, methods, cli, Biobase, SummarizedExperiment, config, golem, shiny, DT, ggplot2, dplyr, rlang, stringr, shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer, logging Suggests: MSnbase, testthat, BiocStyle, knitr, rmarkdown License: Artistic-2.0 MD5sum: 6b52d900a710f2f95ece0c2063710288 NeedsCompilation: no Package: Wrench Version: 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tidyr, SummarizedExperiment Suggests: knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown License: GPL-3 | file LICENSE MD5sum: 030f342990b7bb36dea723fe4871128d NeedsCompilation: no Package: zinbwave Version: 1.33.0 Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats License: Artistic-2.0 MD5sum: 3a506f7afc2995381ff8e18c118dbe53 NeedsCompilation: no Package: zitools Version: 1.5.0 Depends: R (>= 4.4.0), methods Imports: phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment, stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2, reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse, microbiome License: BSD_3_clause + file LICENSE MD5sum: e3db92af3b2719b1cb48ba0bf8ecb803 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