| Depends On Me | ACME, affy, affyPLM, altcdfenvs, amplican, AnnotationDbi, AnnotationForge, AnnotationHub, ATACseqQC, beadarray, bioassayR, Biobase, Biostrings, bnbc, BSgenome, BSgenomeForge, bsseq, Cardinal, Category, categoryCompare, ChAMPdata, chipseq, ChIPseqR, ChromHeatMap, cigarillo, clusterExperiment, codelink, consensusSeekeR, CoreGx, CRISPRseek, cummeRbund, DelayedArray, ensembldb, ExperimentHub, ExperimentHubData, GDSArray, geneplotter, GenomeInfoDb, genomeIntervals, GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges, GenomicScores, ggbio, graph, GSEABase, GUIDEseq, h5mread, HelloRanges, IRanges, ISLET, liftOver, MBASED, MGnifyR, minfi, MLInterfaces, MotifDb, mpra, MSnbase, multtest, NADfinder, ngsReports, oligo, OrganismDbi, pandaR, plyranges, profileplyr, pwalign, PWMEnrich, QSutils, RareVariantVis, REDseq, RnBeads, RPA, rsbml, rsolr, S4Arrays, S4Vectors, Seqinfo, ShortRead, soGGi, SparseArray, spqn, StructuralVariantAnnotation, svaNUMT, svaRetro, TEQC, tigre, topdownr, topGO, txdbmaker, UNDO, updateObject, VanillaICE, VariantAnnotation, VariantFiltering, VCFArray, XVector, yamss |
| Imports Me | a4Preproc, affycoretools, affylmGUI, alabaster.bumpy, alabaster.files, alabaster.matrix, alabaster.ranges, alabaster.se, AllelicImbalance, annmap, annoLinker, annotate, AnnotationHubData, ASpli, ATACseqTFEA, atena, AUCell, autonomics, bambu, bamsignals, BASiCS, batchelor, beachmat, bigmelon, Bioc.gff, BiocBook, biocGraph, BiocHail, BiocIO, BiocSingular, biotmle, biovizBase, biscuiteer, BiSeq, blima, breakpointR, BrowserViz, BubbleTree, bumphunter, BUSpaRse, CAGEfightR, CAGEr, casper, celaref, CellBench, CellMixS, CellTrails, CENTREannotation, CENTREprecomputed, cfDNAPro, cghMCR, ChemmineDrugs, ChemmineOB, ChemmineR, chipenrich, chipenrich.data, ChIPpeakAnno, ChIPQC, ChIPseeker, chipseq, chromVAR, cicero, CircSeqAlignTk, CleanUpRNAseq, clusterSeq, cn.mops, CNEr, CNVPanelizer, CNVRanger, COCOA, cola, compEpiTools, CompoundDb, concordexR, crisprBase, crisprBowtie, crisprBwa, crisprDesign, crispRdesignR, crisprScore, crisprShiny, crisprViz, crlmm, csaw, CTexploreR, cummeRbund, CuratedAtlasQueryR, curatedCRCData, curatedOvarianData, cydar, dada2, dagLogo, DAMEfinder, dandelionR, DCLEAR, ddCt, decompTumor2Sig, deconvR, DegCre, DEGreport, DelayedDataFrame, demuxSNP, derfinder, DEScan2, DESeq2, DESpace, destiny, DEWSeq, DEXSeq, DFplyr, diffcoexp, diffHic, dinoR, DirichletMultinomial, DiscoRhythm, DNAfusion, DOTSeq, dreamlet, DRIMSeq, DropletUtils, DrugVsDisease, easyRNASeq, EBImage, EDASeq, EEMDlstm, eiR, eisaR, ELViS, enhancerHomologSearch, EnrichDO, epialleleR, EpiCompare, epigenomix, epimutacions, epiRomics, epiSeeker, epistack, EpiTxDb, epivizrChart, epivizrStandalone, esATAC, factR, FamAgg, fastseg, ffpe, FindIT2, FLAMES, flowBin, flowClust, flowCore, flowFP, FlowSOM, flowSpecs, flowStats, flowWorkspace, fmcsR, FRASER, frma, GA4GHclient, GA4GHshiny, gcapc, gDNAinRNAseqData, gDNAx, geneAttribution, geneClassifiers, GENESIS, geno2proteo, GenomAutomorphism, GenomicAlignments, GenomicInteractions, GenomicPlot, GenomicTuples, GenVisR, geomeTriD, GeomxTools, GeoMxWorkflows, gINTomics, glmGamPoi, gmapR, gmoviz, GOaGO, goseq, GOTHiC, GSVA, Gviz, HDF5Array, heatmaps, hermes, HicAggR, HiCDOC, HiCExperiment, HiContacts, HiCParser, hicream, HiLDA, hopach, icetea, igblastr, igvR, igvShiny, IHW, IHWpaper, IMAS, infercnv, INSPEcT, InTAD, intansv, InteractionSet, IntEREst, IONiseR, iSEE, IsoformSwitchAnalyzeR, isomiRs, IVAS, KCsmart, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, ldblock, lefser, lemur, linkSet, lisaClust, locuszoomr, LOLA, maaslin3, mariner, maser, MAST, matter, MEAL, meshr, metabinR, MetaboAnnotation, metaMS, metaseqR2, methInheritSim, MethylAid, methylPipe, methylumi, mia, miaViz, microbiomeDataSets, miloR, mimager, MinimumDistance, MIRA, MiRaGE, missMethyl, mist, mobileRNA, Modstrings, mogsa, monaLisa, monocle, Moonlight2R, Motif2Site, motifbreakR, MouseGastrulationData, MouseThymusAgeing, msa, MsBackendSql, MsExperiment, MSnID, MultiAssayExperiment, multicrispr, MultiDataSet, multiMiR, MultimodalExperiment, mumosa, MutationalPatterns, mutscan, MutSeqR, mzR, NanoStringNCTools, ncdfFlow, notame, notameStats, notameViz, npGSEA, nucleR, oligoClasses, oncoPredict, openCyto, openPrimeR, ORFik, OUTRIDER, parati, parglms, pcaMethods, PDATK, pdInfoBuilder, PharmacoGx, PhIPData, PhosR, phyloseq, piano, PIPETS, plyinteractions, podkat, pram, primirTSS, proDA, profileScoreDist, pRoloc, pRolocGUI, ProteoDisco, PSMatch, PureCN, QDNAseq, QFeatures, qPLEXanalyzer, qsea, QTLExperiment, QuasR, R3CPET, R453Plus1Toolbox, RadioGx, raer, raerdata, RaggedExperiment, ramr, ramwas, RCAS, RcisTarget, RCy3, RCyjs, recoup, ReducedExperiment, REMP, ReportingTools, revert, RGSEA, RiboCrypt, RiboDiPA, RiboProfiling, ribosomeProfilingQC, RJMCMCNucleosomes, rnaEditr, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, RNAseqCovarImpute, RNAseqQC, roar, Rqc, Rsamtools, rsbml, rScudo, RTCGAToolbox, rtracklayer, SanityR, saseR, SC3, SCArray.sat, scater, scDblFinder, scDotPlot, scECODA, scmap, scmeth, SCnorm, SCOPE, scPipe, scran, scRNAseq, scruff, scuttle, SEMPLR, SeqVarTools, sevenC, SGSeq, SharedObject, shinyDSP, shinyMethyl, Signac, signatureSearch, signeR, signifinder, simPIC, SingleCellExperiment, SingleR, sitadela, Site2Target, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, snpStats, sparrow, SpatialExperiment, SpatialFeatureExperiment, spatialLIBD, spatzie, Spectra, splatter, SpliceWiz, SplicingGraphs, SplineDV, SQLDataFrame, sRACIPE, sscu, StabMap, standR, strandCheckR, Structstrings, SubtypeDrug, SummarizedExperiment, SVP, SynMut, systemPipeR, systemPipeRdata, tadar, TAPseq, target, TaxaNorm, TCGAutils, TCseq, TENxBUSData, TENxIO, TFBSTools, tidySpatialExperiment, TmCalculator, ToxicoGx, toxpiR, trackViewer, transcriptR, transite, treediff, TreeSummarizedExperiment, tRNA, tRNAscanImport, TSdeeplearning, TVTB, txcutr, Ularcirc, UMI4Cats, unifiedWMWqPCR, UniProt.ws, universalmotif, uSORT, VariantTools, VariantToolsData, velociraptor, vennDiagramLab, VisiumIO, visiumStitched, wavClusteR, weitrix, xcms, XDE, XeniumIO, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, XVector, ZarrArray, zitools |
| Suggests Me | acde, adjclust, adverSCarial, aggregateBioVar, AIMS, AlphaMissenseR, aroma.affymetrix, ASSET, ASURAT, BaalChIP, baySeq, bigmelon, BiocParallel, BiocStyle, biocViews, biosigner, BiRewire, BLMA, BloodGen3Module, bnem, borealis, BUScorrect, BUSseq, CAFE, CAMERA, CausalR, ccrepe, CDI, cellmigRation, CellNOptR, CexoR, chihaya, ChIPanalyser, ChIPXpress, CHRONOS, cleanUpdTSeq, clipper, ClustAll, clustComp, CNORfeeder, CNORfuzzy, ConnectivityMap, consensus, cosmiq, COSNet, cpvSNP, crumblr, cypress, DEsubs, DExMA, DMRcaller, DMRcate, DNAcycP2, DspikeIn, ENCODExplorerData, EnhancedVolcano, ENmix, EpiMix, epiNEM, EventPointer, ExpHunterSuite, fCCAC, fcScan, fgga, FGNet, FieldEffectCrc, flowCut, flowTime, fmrs, GateFinder, gCrisprTools, gdsfmt, GEM, GeneNetworkBuilder, GeneOverlap, geneplast, geneplast.data, geneRxCluster, geNetClassifier, genomation, GEOquery, GeoTcgaData, ggpicrust2, ginmappeR, gkmSVM, GMRP, GOstats, GrafGen, GreyListChIP, grndata, GSEMA, GWASTools, h5vc, Harman, HarmanData, healthyControlsPresenceChecker, HiCDCPlus, hierGWAS, HIREewas, HPiP, hypergraph, iCARE, IFAA, illuminaio, immunotation, inDAGO, InPAS, INPower, IPO, kebabs, KEGGREST, LACE, LRDE, MAGAR, magpie, MarZIC, massiR, MatrixQCvis, MatrixRider, MBttest, mCSEA, Mergeomics, MetaboSignal, metagene2, metagenomeSeq, MetCirc, methylCC, methylInheritance, MetNet, microbiome, microRNAome, miRBaseConverter, miRcomp, mirIntegrator, miRLAB, mnem, MOSClip, motifStack, MsQuality, multiClust, MultiMed, MultiRNAflow, MungeSumstats, MWASTools, ncRNAtools, nempi, NetSAM, nondetects, NoRCE, nucleoSim, omicsGMF, OMICsPCA, OncoScore, PAA, pagoda2, panelcn.mops, Path2PPI, pathMED, PathNet, pathview, PCAtools, pepXMLTab, phenomis, polyRAD, powerTCR, proBAMr, qpgraph, quantro, RBGL, rBiopaxParser, rcellminer, rCGH, REBET, RegParallel, RESOLVE, rfaRm, RFGeneRank, RGraph2js, Rgraphviz, rgsepd, riboSeqR, ROntoTools, ropls, ROSeq, RTN, RTNduals, RTNsurvival, rTRM, SAIGEgds, sangerseqR, SANTA, sarks, SCArray, scDataviz, scLANE, scMultiome, scp, screenCounter, scry, segmentSeq, SeqArray, seqPattern, sesameData, Seurat, SICtools, sigFeature, sigsquared, SIMAT, similaRpeak, SIMLR, singleCellTK, slingshot, SNPRelate, SparseSignatures, spatialHeatmap, specL, STATegRa, STRINGdb, SUITOR, systemPipeTools, TCC, TFEA.ChIP, tidytof, TIN, transcriptogramer, traseR, TreeAndLeaf, tripr, tRNAdbImport, TRONCO, Uniquorn, variancePartition, VERSO, XAItest, xcore, xcoredata, zenith |
, Laurent Gatto [ctb]