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ACE, ADAM, ADAMgui, ADImpute, AffiXcan, affycoretools, aggregateBioVar, AHMassBank, alabaster, alabaster.base, alabaster.bumpy, alabaster.files, alabaster.mae, alabaster.matrix, alabaster.ranges, alabaster.sce, alabaster.schemas, alabaster.se, alabaster.spatial, alabaster.string, alabaster.vcf, ALDEx2, alevinQC, AllelicImbalance, AlpsNMR, AMARETTO, AMOUNTAIN, amplican, AneuFinder, animalcules, annotate, AnnotationDbi, AnnotationFilter, AnnotationForge, AnnotationHub, AnnotationHubData, annotationTools, annotatr, AnVIL, AnVILBilling, AnVILPublish, AnVILWorkflow, APAlyzer, APL, arrayQualityMetrics, artMS, ASGSCA, ASICS, AssessORF, ASSIGN, ATACseqQC, ATACseqTFEA, atena, atSNP, AUCell, autonomics, awst, BaalChIP, bacon, bamsignals, BANDITS, Banksy, banocc, barcodetrackR, basecallQC, BASiCS, basilisk, basilisk.utils, batchelor, BatchQC, bayNorm, baySeq, beachmat, beachmat.hdf5, beadarray, BeadDataPackR, BEARscc, BEclear, beer, benchdamic, BERT, betaHMM, bettr, BG2, BgeeDB, bigmelon, BindingSiteFinder, bioassayR, Biobase, biobtreeR, bioCancer, BioCartaImage, BiocBaseUtils, BiocBook, BiocCheck, BiocFHIR, BiocFileCache, BiocHail, BiocHubsShiny, BiocIO, BiocNeighbors, BioCor, BiocParallel, BiocPkgTools, biocroxytest, BiocSet, BiocSingular, BiocSklearn, biocthis, biocViews, biodb, biodbChebi, biodbExpasy, biodbHmdb, biodbKegg, biodbNcbi, biodbNci, biodbUniprot, biomaRt, biomformat, BioNAR, BioNERO, biosigner, Biostrings, biotmle, biscuiteer, blacksheepr, blima, bluster, bnbc, bnem, BOBaFIT, borealis, branchpointer, breakpointR, brendaDb, BREW3R.r, BridgeDbR, BrowserViz, BSgenomeForge, bsseq, bugsigdbr, BUMHMM, BumpyMatrix, BUScorrect, BUSpaRse, BUSseq, CAFE, CAGEfightR, cageminer, CAGEr, CaMutQC, canceR, cardelino, Cardinal, CardinalIO, CARNIVAL, CATALYST, cbaf, CBEA, cBioPortalData, CBNplot, cbpManager, ccfindR, ccImpute, CCPlotR, ccrepe, CDI, celda, CellBarcode, cellbaseR, CellBench, CelliD, cellity, CellMapper, CellMixS, cellxgenedp, censcyt, CexoR, cfdnakit, 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DaMiRseq, Damsel, DAPAR, dcanr, DCATS, dce, ddPCRclust, debCAM, decompTumor2Sig, decontam, decontX, deconvR, decoupleR, DeepTarget, DEFormats, DegCre, DEGreport, DelayedArray, DelayedDataFrame, DelayedMatrixStats, DelayedRandomArray, DelayedTensor, DELocal, demuxmix, demuxSNP, densvis, DEP, DepecheR, DepInfeR, DeProViR, derfinder, derfinderHelper, derfinderPlot, DEScan2, DESpace, DEWSeq, DExMA, DEXSeq, DIAlignR, DiffBind, diffcyt, DifferentialRegulation, diffuStats, diffUTR, Dino, dir.expiry, discordant, distinct, dittoSeq, DMCFB, DMRScan, dmrseq, DNAfusion, doppelgangR, Doscheda, doseR, doubletrouble, drawProteins, dreamlet, DRIMSeq, DropletUtils, drugTargetInteractions, DSS, dStruct, dupRadar, easier, EasyCellType, easylift, easyreporting, EBImage, EDASeq, edgeR, EGSEA, eiR, eisaR, ELMER, EmpiricalBrownsMethod, ENmix, EnrichmentBrowser, enrichViewNet, ensembldb, EpiDISH, epigraHMM, EpiMix, epimutacions, epiNEM, epiregulon, epiregulon.extra, epistack, epistasisGA, EpiTxDb, epivizr, 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ggkegg, ggmanh, ggmsa, GGPA, ggseqalign, ggspavis, ggtreeSpace, GladiaTOX, Glimma, glmGamPoi, glmSparseNet, GloScope, gmoviz, GMRP, GNOSIS, GOexpress, GOfuncR, GOpro, goSorensen, goSTAG, GOstats, gpuMagic, GrafGen, GRaNIE, granulator, graper, graph, graphite, GreyListChIP, GRmetrics, groHMM, GSAR, gscreend, GSEABase, GSEABenchmarkeR, GSEAmining, GSgalgoR, GSVA, GUIDEseq, Gviz, GWAS.BAYES, gwascat, GWASTools, gwasurvivr, GWENA, gypsum, Harman, hca, HelloRanges, hermes, Herper, HGC, HiCBricks, HiCDOC, HiCExperiment, HiContacts, HiCool, hicVennDiagram, HiLDA, hipathia, HIREewas, HiTC, hoodscanR, HPAanalyze, hpar, HPiP, HTSFilter, hummingbird, HybridExpress, ideal, IFAA, iGC, IgGeneUsage, igvR, igvShiny, IHW, illuminaio, ILoReg, IMAS, imcRtools, immunoClust, immunotation, infercnv, Informeasure, InPAS, INSPEcT, INTACT, InTAD, InteractionSet, InterCellar, IONiseR, iPath, IRanges, ISAnalytics, iSEE, iSEEde, iSEEfier, iSEEhex, iSEEhub, iSEEindex, iSEEpathways, iSEEu, ISLET, IsoBayes, 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missRows, mistyR, mixOmics, MLInterfaces, MMDiff2, MMUPHin, mnem, moanin, mobileRNA, MODA, Modstrings, MOFA2, mogsa, MoleculeExperiment, MOMA, monaLisa, Moonlight2R, MoonlightR, mosbi, mosdef, MOSim, Motif2Site, motifbreakR, MotifDb, motifStack, motifTestR, MouseFM, mpra, MSA2dist, MsBackendMassbank, MsBackendMgf, MsBackendMsp, MsBackendRawFileReader, MsBackendSql, MsCoreUtils, MsDataHub, MsExperiment, MsFeatures, msImpute, mslp, MSnbase, MSPrep, msPurity, msqrob2, MsQuality, MSstats, MSstatsLiP, MSstatsLOBD, MSstatsTMT, MuData, MultiAssayExperiment, MultiBaC, multicrispr, MultiDataSet, multiGSEA, multiHiCcompare, multiMiR, MultimodalExperiment, MultiRNAflow, multistateQTL, multiWGCNA, mumosa, MungeSumstats, muscat, musicatk, MutationalPatterns, MWASTools, mygene, myvariant, mzR, NADfinder, NanoMethViz, NanoStringDiff, ncGTW, ncRNAtools, ndexr, Nebulosa, nempi, NetActivity, netDx, nethet, netprioR, netSmooth, NeuCA, NewWave, ngsReports, nipalsMCIA, nnSVG, NormalyzerDE, normr, NPARC, npGSEA, nucleoSim, nucleR, oligo, omicade4, omicRexposome, omicsPrint, omicsViewer, Omixer, oncoscanR, OncoScore, OncoSimulR, optimalFlow, OPWeight, ORFhunteR, ORFik, OrganismDbi, Organism.dplyr, orthogene, orthos, Oscope, OUTRIDER, OutSplice, OVESEG, PAA, packFinder, padma, PAIRADISE, pairedGSEA, pairkat, PanomiR, PanViz, pareg, parglms, parody, partCNV, Path2PPI, pathlinkR, paxtoolsr, pcaExplorer, PCAN, PDATK, PeacoQC, peakPantheR, Pedixplorer, PepsNMR, pfamAnalyzeR, pgxRpi, phantasus, phantasusLite, PharmacoGx, phenomis, phenopath, philr, PhIPData, PhosR, phyloseq, piano, pipeComp, PIPETS, Pirat, PIUMA, planttfhunter, plasmut, plotGrouper, plyinteractions, plyranges, pmp, PoDCall, POMA, powerTCR, POWSC, ppcseq, pqsfinder, pram, preciseTAD, PrInCE, proDA, profileplyr, profileScoreDist, progeny, projectR, pRoloc, pRolocGUI, Prostar, ProteoDisco, ProteoMM, PSMatch, psygenet2r, ptairMS, PureCN, PWMEnrich, qcmetrics, QDNAseq, QFeatures, qmtools, qpgraph, qsea, qsmooth, QSutils, qsvaR, QTLExperiment, Qtlizer, quantiseqr, quantro, QuasR, R3CPET, RadioGx, raer, RaggedExperiment, RAIDS, rain, ramwas, randRotation, RAREsim, Rarr, rawDiag, rawrr, RBGL, RBioFormats, Rbowtie, Rbwa, rcellminer, rCGH, RcisTarget, Rcollectl, RCSL, Rcwl, RcwlPipelines, RCX, RCy3, RCyjs, ReactomePA, recount, recount3, recountmethylation, recoup, RedeR, RedisParam, regionalpcs, RegionalST, regioneR, regioneReloaded, regsplice, regutools, ResidualMatrix, RESOLVE, retrofit, ReUseData, rexposome, rfaRm, Rfastp, rfPred, RGMQL, RgnTX, rgoslin, RGraph2js, RGSEA, rhdf5, rhdf5client, rhdf5filters, Rhdf5lib, Rhisat2, Rhtslib, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, rifi, rifiComparative, RIVER, RJMCMCNucleosomes, RMassBank, rmspc, RNAmodR, RNAmodR.AlkAnilineSeq, RNAmodR.ML, RNAmodR.RiboMethSeq, rnaseqcomp, RNAseqCovarImpute, RnaSeqSampleSize, Rnits, roastgsa, ROC, ROCpAI, rols, ropls, rprimer, rpx, rrvgo, Rsamtools, rScudo, rsemmed, rSWeeP, RTCGAToolbox, RTN, RTNduals, RTNsurvival, Rtpca, rTRM, RUVSeq, Rvisdiff, RVS, rWikiPathways, S4Arrays, S4Vectors, sampleClassifier, sangerseqR, satuRn, SC3, ScaledMatrix, scanMiR, scanMiRApp, SCArray.sat, scater, scBubbletree, scCB2, sccomp, scDblFinder, scDD, scDDboost, scDesign3, scds, SCFA, scFeatureFilter, scFeatures, scifer, scmap, scMerge, scMitoMut, SCnorm, scone, scoreInvHap, scp, scPCA, scPipe, scran, scReClassify, screenCounter, ScreenR, scRepertoire, scRNAseqApp, scruff, scTHI, scTreeViz, scuttle, scviR, sechm, segmentSeq, selectKSigs, seqArchR, seqArchRplus, seqCAT, SeqGate, seq.hotSPOT, seqLogo, seqPattern, seqsetvis, SeqSQC, SeqVarTools, sesame, SEtools, sevenC, SGSeq, SharedObject, shinyepico, shinyMethyl, ShortRead, SIAMCAT, SigCheck, SigFuge, signatureSearch, SigsPack, SIMD, SimFFPE, similaRpeak, SIMLR, simPIC, simpleSeg, sincell, SingleCellAlleleExperiment, SingleCellExperiment, singleCellTK, SingleR, singscore, SiPSiC, sitadela, sitePath, sketchR, slalom, slingshot, SMAD, smartid, smoothclust, snapcount, snifter, SNPediaR, SNPhood, soGGi, SOMNiBUS, SpaceMarkers, SparseArray, sparseMatrixStats, sparsenetgls, SparseSignatures, spaSim, SpatialCPie, spatialDE, SpatialExperiment, SpatialFeatureExperiment, spatialHeatmap, speckle, specL, Spectra, SpectralTAD, SPIAT, spicyR, spillR, splatter, SPLINTER, splots, SpotClean, SPOTlight, SpotSweeper, spqn, SPsimSeq, SQLDataFrame, sRACIPE, srnadiff, sSNAPPY, ssrch, stageR, STATegRa, Statial, statTarget, STdeconvolve, stJoincount, strandCheckR, struct, Structstrings, structToolbox, SubCellBarCode, SUITOR, SummarizedExperiment, sva, svaRetro, SVMDO, swfdr, switchde, synapsis, synapter, SynExtend, synlet, syntenet, systemPipeR, systemPipeShiny, systemPipeTools, tadar, TADCompare, tanggle, TAPseq, TargetDecoy, TargetSearch, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TDbasedUFE, TDbasedUFEadv, TEKRABber, TENxIO, terraTCGAdata, TFARM, TFBSTools, TFHAZ, TFutils, tidybulk, tidyCoverage, tidyFlowCore, tidySingleCellExperiment, tidySpatialExperiment, tidySummarizedExperiment, tigre, TileDBArray, timeOmics, TMixClust, TOAST, tomoda, tomoseqr, TOP, topconfects, topdownr, ToxicoGx, TPP2D, TPP, tpSVG, tracktables, trackViewer, TrajectoryUtils, transcriptogramer, transcriptR, transformGamPoi, transmogR, transomics2cytoscape, TreeAndLeaf, treeclimbR, treekoR, TreeSummarizedExperiment, TREG, Trendy, tricycle, tripr, tRNA, tRNAdbImport, tRNAscanImport, TRONCO, TTMap, TurboNorm, twoddpcr, txcutr, txdbmaker, UCell, UCSC.utils, Ularcirc, UMI4Cats, uncoverappLib, UniProt.ws, UPDhmm, variancePartition, VariantAnnotation, VariantExperiment, VariantFiltering, VCFArray, VDJdive, velociraptor, VERSO, vidger, ViSEAGO, VisiumIO, vissE, Voyager, vsclust, vsn, wateRmelon, wavClusteR, weitrix, wpm, xcms, xcore, Xeva, XNAString, yamss, YAPSA, zellkonverter, zenith, zinbwave, zlibbioc, ZygosityPredictor, AHEnsDbs, AHLRBaseDbs, AHMeSHDbs, AHPathbankDbs, AHPubMedDbs, AHWikipathwaysDbs, AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, ath1121501frmavecs, cadd.v1.6.hg19, cadd.v1.6.hg38, CTCF, EpiTxDb.Hs.hg38, EpiTxDb.Mm.mm10, EpiTxDb.Sc.sacCer3, EuPathDB, excluderanges, geneplast.data, GenomicState, hpAnnot, JASPAR2022, JASPAR2024, phastCons35way.UCSC.mm39, phyloP35way.UCSC.mm39, rat2302frmavecs, SomaScan.db, synaptome.data, UCSCRepeatMasker, ASICSdata, benchmarkfdrData2019, BioImageDbs, BioPlex, blimaTestingData, BloodCancerMultiOmics2017, bodymapRat, brgedata, CardinalWorkflows, celldex, CellMapperData, cfToolsData, chipenrich.data, ChIPexoQualExample, chipseqDBData, CLLmethylation, clustifyrdatahub, CopyhelpeR, COSMIC.67, crisprScoreData, curatedBladderData, curatedMetagenomicData, curatedOvarianData, curatedPCaData, curatedTBData, curatedTCGAData, CytoMethIC, DAPARdata, depmap, derfinderData, DExMAdata, DmelSGI, DNAZooData, dorothea, DropletTestFiles, DuoClustering2018, easierData, ELMER.data, emtdata, epimutacionsData, ewceData, fourDNData, furrowSeg, gDNAinRNAseqData, gDRtestData, GenomicDistributionsData, GeuvadisTranscriptExpr, GSE103322, GSE13015, GSE159526, GSE62944, HarmanData, HCAData, HCATonsilData, HD2013SGI, HDCytoData, healthyControlsPresenceChecker, HelloRangesData, HiCDataHumanIMR90, HiContactsData, HighlyReplicatedRNASeq, Hiiragi2013, HMP16SData, HMP2Data, HumanAffyData, IHWpaper, imcdatasets, JohnsonKinaseData, LRcellTypeMarkers, mCSEAdata, mcsurvdata, MerfishData, MetaGxOvarian, MetaGxPancreas, MetaScope, MethylAidData, methylclockData, MethylSeqData, MicrobiomeBenchmarkData, microbiomeDataSets, minionSummaryData, MOFAdata, MouseAgingData, MouseGastrulationData, MouseThymusAgeing, msigdb, MSMB, msqc1, multiWGCNAdata, muscData, nanotubes, NestLink, NetActivityData, OnassisJavaLibs, optimalFlowData, orthosData, parathyroidSE, pasilla, PasillaTranscriptExpr, PCHiCdata, PepsNMRData, preciseTADhub, ptairData, raerdata, rcellminerData, RforProteomics, RGMQLlib, RNAmodR.Data, RnaSeqSampleSizeData, sampleClassifierData, scaeData, scanMiRData, scATAC.Explorer, SCLCBam, scMultiome, scpdata, scRNAseq, seventyGeneData, SFEData, SimBenchData, Single.mTEC.Transcriptomes, SingleCellMultiModal, smokingMouse, SpatialDatasets, spatialDmelxsim, spatialLIBD, STexampleData, SubcellularSpatialData, systemPipeRdata, TabulaMurisData, TabulaMurisSenisData, tartare, TCGAbiolinksGUI.data, TCGAWorkflowData, TENxBrainData, TENxBUSData, TENxPBMCData, TENxVisiumData, TENxXeniumData, timecoursedata, TimerQuant, tissueTreg, TMExplorer, TransOmicsData, tuberculosis, tweeDEseqCountData, VariantToolsData, VectraPolarisData, WeberDivechaLCdata, zebrafishRNASeq, annotation, arrays, BiocMetaWorkflow, CAGEWorkflow, chipseqDB, csawUsersGuide, EGSEA123, ExpressionNormalizationWorkflow, generegulation, highthroughputassays, liftOver, maEndToEnd, recountWorkflow, RNAseq123, seqpac, sequencing, SingscoreAMLMutations, variants, aIc, asteRisk, BiocManager, BOSO, corrmeta, cyjShiny, EHRtemporalVariability, ggBubbles, ipsRdbs, magmaR, MarZIC, MetaIntegrator, multiclassPairs, MVN, net4pg, NutrienTrackeR, openSkies, PlackettLuce, Rediscover, rjsoncons, rworkflows, SNPassoc, StepReg, TFactSR |
, Mike Smith [ctb]