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Bioconductor 3.23

Bioconductor 3.23 Packages

All packages — 3805

Package	Title
a4Software	Automated Affymetrix Array Analysis Umbrella Package
a4BaseSoftware	Automated Affymetrix Array Analysis Base Package
a4ClassifSoftware	Automated Affymetrix Array Analysis Classification Package
a4CoreSoftware	Automated Affymetrix Array Analysis Core Package
a4PreprocSoftware	Automated Affymetrix Array Analysis Preprocessing Package
a4ReportingSoftware	Automated Affymetrix Array Analysis Reporting Package
ABarraySoftware	Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
abseqRSoftware	Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
ABSSeqSoftware	ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
acdeSoftware	Artificial Components Detection of Differentially Expressed Genes
ACESoftware	Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
aCGHSoftware	Classes and functions for Array Comparative Genomic Hybridization data
ACMESoftware	Algorithms for Calculating Microarray Enrichment (ACME)
ADaCGH2Software	Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects
ADAMSoftware	ADAM: Activity and Diversity Analysis Module
ADAMguiSoftware	Activity and Diversity Analysis Module Graphical User Interface
ADAPTSoftware	Analysis of Microbiome Differential Abundance by Pooling Tobit Models
adductDataExperiment	Data from untargeted MS of modifications to Cys34 of serum albumin
adductomicsRSoftware
ADImputeSoftware	Adaptive Dropout Imputer (ADImpute)
adme16cod.dbAnnotation	Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)
adSplitSoftware	Annotation-Driven Clustering
adverSCarialSoftware	adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks
AerithSoftware	visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics
AffiXcanSoftware	A Functional Approach To Impute Genetically Regulated Expression
affxparserSoftware	Affymetrix File Parsing SDK
affySoftware	Methods for Affymetrix Oligonucleotide Arrays
affycompSoftware	Graphics Toolbox for Assessment of Affymetrix Expression Measures
affycompDataExperiment	affycomp data
affyContamSoftware	structured corruption of affymetrix cel file data
affycoretoolsSoftware	Functions useful for those doing repetitive analyses with Affymetrix GeneChips
affydataExperiment	Affymetrix Data for Demonstration Purpose
Affyhgu133A2ExprExperiment	Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package
Affyhgu133aExprExperiment	Affymetrix Human hgu133a Array (GPL96) Expression Data Package
Affyhgu133Plus2ExprExperiment	Affyhgu133Plus2Expr (GPL570) Expression Data Package
affyILMSoftware	Linear Model of background subtraction and the Langmuir isotherm
affyioSoftware	Tools for parsing Affymetrix data files
affylmGUISoftware	GUI for limma Package with Affymetrix Microarrays
AffymetrixDataTestFilesExperiment	Affymetrix Data Files (CEL, CDF, CHP, EXP, PGF, PSI) for Testing
Affymoe4302ExprExperiment	Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package
affyPLMSoftware	Methods for fitting probe-level models
AffyRNADegradationSoftware	Analyze and correct probe positional bias in microarray data due to RNA degradation
ag.dbAnnotation	Affymetrix Affymetrix AG Array annotation data (chip ag)
agcdfAnnotation	agcdf
AGDEXSoftware	Agreement of Differential Expression Analysis
aggregateBioVarSoftware	Differential Gene Expression Analysis for Multi-subject scRNA-seq
agilpSoftware	Agilent expression array processing package
AgiMicroRnaSoftware	Processing and Differential Expression Analysis of Agilent microRNA chips
agprobeAnnotation	Probe sequence data for microarrays of type ag
AHCytoBandsAnnotation	CytoBands for AnnotationHub
AHEnsDbsAnnotation	EnsDbs for AnnotationHub
AHLRBaseDbsAnnotation	LRBaseDbs for AnnotationHub
AHMassBankSoftware	MassBank Annotation Resources for AnnotationHub
AHMeSHDbsAnnotation	MeSHDbs for AnnotationHub
AHPathbankDbsAnnotation	Metabolites and proteins linked to PathBank pathways (for AnnotationHub)
AHPubMedDbsAnnotation	SQLites, tibbles, and data.tables for AnnotationHub
AHWikipathwaysDbsAnnotation	Metabolites linked to WikiPathways pathways (for AnnotationHub)
AIMSSoftware	AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
airpartSoftware	Differential cell-type-specific allelic imbalance
airwayExperiment	RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
alabasterSoftware	Umbrella for the Alabaster Framework
alabaster.baseSoftware	Save Bioconductor Objects to File
alabaster.bumpySoftware	Save and Load BumpyMatrices to/from file
alabaster.filesSoftware	Wrappers to Save Common File Formats
alabaster.maeSoftware	Load and Save MultiAssayExperiments
alabaster.matrixSoftware	Load and Save Artifacts from File
alabaster.rangesSoftware	Load and Save Ranges-related Artifacts from File
alabaster.sceSoftware	Load and Save SingleCellExperiment from File
alabaster.schemasSoftware	Schemas for the Alabaster Framework
alabaster.seSoftware	Load and Save SummarizedExperiments from File
alabaster.sfeSoftware	Language agnostic on disk serialization of SpatialFeatureExperiment
alabaster.spatialSoftware	Save and Load Spatial 'Omics Data to/from File
alabaster.stringSoftware	Save and Load Biostrings to/from File
alabaster.vcfSoftware	Save and Load Variant Data to/from File
ALDEx2Software	Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
alevinQCSoftware	Generate QC Reports For Alevin Output
ALLExperiment	A data package
AllelicImbalanceSoftware	Investigates Allele Specific Expression
ALLMLLExperiment	A subset of arrays from a large acute lymphoblastic leukemia (ALL) study
AlphaBetaSoftware	Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
AlphaMissense.v2023.hg19Annotation	AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19
AlphaMissense.v2023.hg38Annotation	AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg38
AlphaMissenseRSoftware	Accessing AlphaMissense Data Resources in R
AlpsNMRSoftware	Automated spectraL Processing System for NMR
altcdfenvsSoftware	alternative CDF environments (aka probeset mappings)
alternativeSplicingEvents.hg19Annotation	Alternative splicing event annotation for Human (hg19)
alternativeSplicingEvents.hg38Annotation	Alternative splicing event annotation for Human (hg38)
AMARETTOSoftware	Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
AMOUNTAINSoftware	Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
AmpAffyExampleExperiment	Example of Amplified Data
amplicanSoftware	Automated analysis of CRISPR experiments
anansiSoftware	Annotation-Based Analysis of Specific Interactions
AnaquinSoftware	Statistical analysis of sequins
ANCOMBCSoftware	Microbiome differential abudance and correlation analyses with bias correction
ANFSoftware	Affinity Network Fusion for Complex Patient Clustering
anglemaniaSoftware	Feature Extraction for scRNA-seq Dataset Integration
animalculesSoftware	Interactive microbiome analysis toolkit
annaffySoftware	Annotation tools for Affymetrix biological metadata
anndataRSoftware	AnnData interoperability in R
annmapSoftware	Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Browse packages by biocViews term. Counts are cumulative over each subtree.

Software (2418)

a4 a4Base a4Classif a4Core a4Preproc a4Reporting ABarray abseqR ABSSeq acde ACE aCGH ACME ADaCGH2 ADAM ADAMgui ADAPT adductomicsR ADImpute adSplit adverSCarial Aerith AffiXcan affxparser affy affycomp affyContam affycoretools affyILM affyio affylmGUI affyPLM AffyRNADegradation AGDEX aggregateBioVar agilp AgiMicroRna AHMassBank AIMS airpart alabaster alabaster.base alabaster.bumpy alabaster.files alabaster.mae alabaster.matrix alabaster.ranges alabaster.sce alabaster.schemas alabaster.se alabaster.sfe alabaster.spatial alabaster.string alabaster.vcf ALDEx2 alevinQC AllelicImbalance AlphaBeta AlphaMissenseR AlpsNMR altcdfenvs AMARETTO AMOUNTAIN amplican anansi Anaquin ANCOMBC ANF anglemania animalcules annaffy anndataR annmap annoLinker annotate AnnotationDbi AnnotationFilter AnnotationForge AnnotationHub AnnotationHubData annotationTools annotatr anota anota2seq antiProfiles AnVIL AnVILAz AnVILBase AnVILBilling AnVILGCP AnVILPublish AnVILWorkflow APAlyzer apComplex apeglm APL appreci8R aroma.light ArrayExpress arrayMvout arrayQuality arrayQualityMetrics ARRmNormalization artMS ASAFE ASEB ASGSCA ASICS ASpli AssessORF ASSET ASSIGN assorthead ASURAT asuri atacInferCnv ATACseqQC ATACseqTFEA atena atSNP attract AUCell autonomics AWAggregator AWFisher awst BaalChIP bacon BADER BadRegionFinder BAGS ballgown bambu bamsignals BANDITS bandle Banksy banocc barbieQ barcodetrackR basecallQC BaseSpaceR Basic4Cseq BASiCS BASiCStan BasicSTARRseq basilisk basilisk.utils batchCorr BatChef batchelor BatchQC BatchSVG Battlefield BayesKnockdown BayesSpace bayNorm baySeq BBCAnalyzer BCRANK bcSeq beachmat beachmat.hdf5 beachmat.tiledb beadarray BeadDataPackR BEAT BEclear bedbaser beer benchdamic BERT betaHMM betterChromVAR bettr BG2 BgeeCall BgeeDB BicARE BiFET bigmelon BindingSiteFinder bioassayR Biobase biobroom biobtreeR Bioc.gff bioCancer BioCartaImage BiocAzul BiocBaseUtils BiocBook BiocBuildReporter BiocCheck BiocFHIR BiocFileCache BiocGenerics biocGraph BiocHail BiocHubsShiny BiocIO BiocMaintainerApp biocmake BiocNeighbors BioCor BiocParallel BiocPkgDash BiocPkgTools biocroxytest BiocSet BiocSingular BiocSklearn BiocStyle biocthis BiocVersion biocViews BiocWorkflowTools biodb biodbChebi bioDist BioGA biomaRt biomformat BioMVCClass biomvRCNS BioNAR BioNERO BioNet BioQC biosigner Biostrings BioTIP biotmle biovizBase BiRewire biscuiteer BiSeq blacksheepr blase blima BLMA BloodGen3Module bluster bnbc bnem BOBaFIT borealis BPRMeth BRAIN branchpointer breakpointR BreastSubtypeR brendaDb BREW3R.r BridgeDbR broadSeq BrowserViz BSgenome BSgenomeForge bsseq BubbleTree BufferedMatrix BufferedMatrixMethods bugsigdbr BulkSignalR BUMHMM bumphunter BumpyMatrix BUS BUScorrect BUSpaRse BUSseq CaDrA CAEN CAFE CAGEfightR cageminer CAGEr CalibraCurve calm CAMERA CaMutQC canceR cancerclass cardelino Cardinal CardinalIO CARDspa carnation CARNIVAL casper CATALYST Category categoryCompare CatsCradle CausalR cbaf cBioPortalData CBN2Path CBNplot cbpManager CCAFE ccfindR ccImpute CCPlotR CCPROMISE ccrepe CDI celaref celda CellBarcode cellbaseR CellBench CelliD cellity CellMapper CellMentor cellmig cellmigRation CellMixS CellNOptR cellscape CellTrails cellxgenedp CEMiTool censcyt Cepo ceRNAnetsim CeTF CexoR CFAssay cfdnakit cfDNAPro cfTools CGEN CGHbase CGHcall cghMCR CGHnormaliter CGHregions ChAMP ChemmineOB ChemmineR CHETAH chevreulPlot chevreulProcess chevreulShiny Chicago chihaya chimeraviz ChIPanalyser ChIPComp chipenrich ChIPexoQual ChIPpeakAnno ChIPQC ChIPseeker chipseq ChIPseqR ChIPsim ChIPXpress chopsticks Chromatograms chromDraw ChromHeatMap chromPlot ChromSCape chromVAR CHRONOS cicero cigarillo CIMICE circRNAprofiler CircSeqAlignTk CiteFuse ClassifyR cleanUpdTSeq CleanUpRNAseq cleaver clevRvis clippda clipper cliProfiler cliqueMS Clomial ClonalSim clst clstutils CluMSID ClustAll clustComp clusterExperiment ClusterFoldSimilarity ClusterGVis ClusterJudge clusterProfiler clusterSeq ClusterSignificance clusterStab clustifyr ClustIRR clustSIGNAL CMA cmapR cn.farms cn.mops CNAnorm CNEr CNORdt CNORfeeder CNORfuzzy CNORode CNTools CNVfilteR cnvGSA CNViz CNVMetrics CNVPanelizer CNVRanger CNVrd2 CoCiteStats COCOA codelink CODEX CoGAPS cogena cogeqc Cogito coGPS cola comapr combi coMethDMR COMPASS compcodeR CompensAID compEpiTools ComplexHeatmap CompoundDb ComPrAn compSPOT concordexR condiments CONFESS consensus ConsensusClusterPlus consensusDE consensusOV consensusSeekeR consICA CONSTANd conumee convert copa CopyNumberPlots Coralysis coRdon CoreGx Cormotif corral coseq CoSIA cosmiq cosmosR COSNet COTAN countsimQC covEB CoverageView covRNA CPSM cpvSNP cqn CrcBiomeScreen CRImage CRISPRball crisprBase crisprBowtie crisprBwa crisprDesign crisprScore CRISPRseek crisprShiny CrispRVariants crisprVerse crisprViz crlmm crumblr crupR CSAR csaw csdR CSOA CSSQ ctc CTdata CTDquerier CTexploreR cTRAP ctsGE CTSV cummeRbund CuratedAtlasQueryR customCMPdb customProDB cyanoFilter cycle cydar cypress CytoDx CyTOFpower cytofQC CytoGLMM cytoKernel cytolib cytomapper CytoMDS cytoMEM CytoML CytoPipeline CytoPipelineGUI cytoviewer dada2 dagLogo daMA DAMEfinder damidBind DaMiRseq Damsel dandelionR DAPAR dar DART dcanr DCATS dcGSA ddCt ddPCRclust dearseq debCAM debrowser decemedip DECIPHER decompTumor2Sig DeconRNASeq decontam decontX DeconvoBuddies deconvR decoupleR DeeDeeExperiment DeepPINCS deepSNV DeepTarget DEFormats DegCre DegNorm DEGraph DEGreport DEGseq DelayedArray DelayedDataFrame DelayedMatrixStats DelayedRandomArray DelayedTensor DELocal deltaCaptureC deltaGseg DeMAND DeMixT demuxmix demuxSNP DenoIST densvis DepecheR DepInfeR DEqMS derfinder derfinderHelper derfinderPlot DEScan2 DESeq2 DEsingle DESpace destiny DEsubs DEWSeq DExMA DEXSeq DFP DFplyr DiffBind diffcoexp diffcyt DifferentialRegulation diffGeneAnalysis diffHic DiffLogo diffuStats diffUTR diggit Dino dinoR dir.expiry DirichletMultinomial discordant DiscoRhythm distinct dittoSeq divergence dks DMCFB DMCHMM dmGsea DMRcaller DMRcate DMRScan dmrseq DNABarcodeCompatibility DNABarcodes DNAcopy DNAcycP2 DNAfusion DNAshapeR DNEA dominatR DominoEffect dominoSignal doppelgangR Doscheda DOSE doseR DOtools DOTSeq doubletrouble drawProteins dreamlet DRIMSeq DriverNet DropletUtils drugfindR drugTargetInteractions DrugVsDisease DspikeIn DSS dStruct DTA Dune DuplexDiscovereR dupRadar dyebias DynDoc easier EasyCellType easylift easyreporting easyRNASeq EBarrays EBcoexpress EBImage EBSEA EBSeq ecolitk EDASeq edge edgeR EDIRquery eds EGAD EGSEA eiR eisaR ELMER ELViS EMDomics EmpiricalBrownsMethod EnhancedVolcano enhancerHomologSearch EnMCB ENmix EnrichDO EnrichedHeatmap EnrichmentBrowser enrichplot enrichViewNet ensembldb epialleleR EpiCompare epidecodeR EpiDISH epigenomix epigraHMM EpiMix epimutacions epiNEM EpipwR epiregulon epiregulon.extra epiRomics epiSeeker epistack epistasisGA EpiTxDb epivizr epivizrChart epivizrData epivizrServer epivizrStandalone erccdashboard ERSSA esATAC escape escheR esetVis eudysbiome evaluomeR EventPointer EWCE ExCluster ExiMiR ExperimentHub ExperimentHubData ExperimentSubset ExploreModelMatrix ExpoRiskR ExpressionAtlas extraChIPs fabia factDesign factR faers FamAgg famat fastLiquidAssociation FastqCleaner fastRanges fastreeR fastseg fCCAC fCI fcScan fdrame FEAST FeatSeekR fedup FELLA fenr ffpe fgga FGNet fgsea FilterFFPE findIPs FindIT2 FinfoMDS FISHalyseR fishpond FitHiC flagme FLAMES flowAI flowBeads flowBin flowcatchR flowCHIC flowClean flowClust flowCore flowCut flowCyBar flowDensity flowFP flowGate flowGraph flowMatch flowMeans flowMerge flowPeaks flowPloidy flowPlots FlowSOM flowSpecs flowStats flowTime flowTrans flowViz flowVS flowWorkspace fmcsR fmrs fobitools fourSynergy fRagmentomics fraq FRASER frenchFISH FRGEpistasis frma frmaTools funOmics funtooNorm FuseSOM G4SNVHunter GA4GHclient GA4GHshiny gaga gage GAprediction garfield GARS GateFinder gatom GBScleanR gcapc gcatest GCPtools gCrisprTools gcrma GDCRNATools gDNAx gDR gDRcore gDRimport gDRstyle gDRutils GDSArray gdsfmt GeDi GEM gemini gemma.R genArise geneAttribution GeneBreak geneClassifiers GeneExpressionSignature genefilter genefu GeneGA GeneMeta GeneNetworkBuilder GeneOverlap geneplast geneplotter geneRecommender GeneRegionScan geneRxCluster GeneSelectMMD GENESIS GeneStructureTools geNetClassifier GeneticsPed GeneTonic geneXtendeR GENIE3 genomation GenomAutomorphism GenomeInfoDb genomeIntervals genomes GenomicAlignments GenomicCoordinates GenomicDataCommons GenomicDistributions GenomicFeatures GenomicFiles genomicInstability GenomicInteractionNodes GenomicInteractions GenomicOZone GenomicPlot GenomicRanges GenomicScores GenomicSuperSignature GenomicTuples GenProSeq GenVisR GeoDiff GEOexplorer GEOfastq GEOmetadb geomeTriD GeomxTools GEOquery GEOsubmission GeoTcgaData gep2pep getDEE2 geva GEWIST geyser gg4way ggbio ggcyto ggkegg ggmanh ggmsa GGPA ggsc ggseqalign ggspavis ggtree ggtreeDendro ggtreeExtra ggtreeSpace GIGSEA ginmappeR gINTomics GLAD GladiaTOX Glimma glmGamPoi glmSparseNet GlobalAncova globalSeq globaltest GloScope glycoTraitR gmapR GmicR gmoviz GMRP GNET2 GNOSIS GOaGO goatea GOexpress GOfan GOfuncR GOpro goProfiles GOSemSim goseq goSorensen goSTAG GOstats GOTHiC goTools GPA gpls GrafGen GRaNIE granulator graper graph GraphAlignment GraphAT GraphExperiment graphite GRENITS GreyListChIP GRmetrics groHMM GSABenchmark GSALightning GSAR GSCA gscreend GSEABase GSEABenchmarkeR GSEAlm GSEAmining gsean GSgalgoR GSReg GSRI GSVA gtrellis GUIDEseq Guitar gVenn Gviz GWAS.BAYES gwascat GWASTools gwasurvivr GWENA gypsum h5mread h5vc hammers hapFabia Harman HarmonizR hca HDF5Array HDTD hdxmsqc heatmaps Heatplus HelloRanges HELP HEM hermes HERON Herper HGC HIBAG HicAggR HiCaptuRe HiCBricks HiCcompare HiCDCPlus HiCDOC HiCExperiment HiContacts HiCool HiCParser HiCPotts hicVennDiagram hierGWAS hierinf HilbertCurve HilbertVis HilbertVisGUI HiLDA hipathia HIPPO HIREewas HiSpaR HistoImagePlot HiTC hmdbQuery HMMcopy HoloFoodR hoodscanR hopach HPAanalyze hpar HPiP HTqPCR HTSFilter HuBMAPR HubPub hummingbird HVP HybridExpress HybridMTest hypeR hyperdraw hypergraph iASeq iasva iBBiG Ibex ibh iBMQ iCARE Icens icetea iCheck iChip iClusterPlus iCNV iCOBRA ideal IdeoViz idiogram idpr idr2d IFAA igblastr iGC IgGeneUsage igvR igvShiny IHW illuminaio ILoReg ImageArray imageFeatureTCGA imageTCGA imageTCGAutils IMAS imcRtools IMMAN immApex immLynx immReferent immunoClust immunogenViewer immunotation iModMix IMPCdata impute INDEED iNETgrate infercnv infinityFlow Informeasure InPAS INPower INSPEcT INTACT InTAD intansv interacCircos InteractionSet InteractiveComplexHeatmap InterCellar IntEREst IntramiRExploreR IONiseR iPath ipdDb IPO IRanges ISAnalytics iscream iSEE iSEEde iSEEfier iSEEhex iSEEhub iSEEindex iSEEpathways iSEEtree iSEEu iSeq ISLET islify isobar IsoBayes IsoCorrectoR IsoCorrectoRGUI IsoformSwitchAnalyzeR ISoLDE isomiRs ITALICS iterativeBMA iterativeBMAsurv IVAS ivygapSE IWTomics jazzPanda jvecfor karyoploteR katdetectr KBoost KCsmart kebabs KEGGgraph KEGGlincs keggorthology KEGGREST KinSwingR kissDE kmcut KnowSeq knowYourCG koinar LACE LACHESIS LBE lcmsPlot ldblock LEA leapR LedPred lefser lemur les levi lfa Lheuristic limma limmaGUI limpa limpca LimROTS lineagespot LinkHD linkSet Linnorm lionessR lipidr LipidTrend LiquidAssociation lisaClust lmdme lncRna LOBSTAHS loci2path logicFS LOLA looking4clusters LoomExperiment LPE lpNet lpsymphony LRBaseDbi LRcell LRDE lumi LymphoSeq M3C M3Drop m6Aboost Maaslin2 maaslin3 Macarron maCorrPlot MACSQuantifyR MACSr made4 maftools MAGAR magpie magrene MAI MAIT makecdfenv MANOR MantelCorr MAPFX maPredictDSC mapscape mariner markeR marr marray martini maser maSigPro maskBAD MassArray massiR MassSpecWavelet MAST mastR matchBox MatrixGenerics MatrixQCvis MatrixRider matter MBAmethyl MBASED MBCB MBECS mbkmeans mBPCR MBQN mbQTL MBttest MCbiclust mCSEA mdp mdqc MDSvis MDTS MEAL MeasurementError.cor MEAT MEB MEDIPS MEDME megadepth MEIGOR Melissa MeLSI memes Mergeomics MeSHDbi meshes meshr MesKit messina metabCombiner metabinR MetaboAnnotation MetaboAnnotatoR MetaboCoreUtils MetaboDynamics metabolomicsWorkbenchR metabom8 metabomxtr MetaboSignal metaCCA MetaCyto MetaDICT metagene2 metagenomeSeq metahdep metaMS MetaNeighbor MetaPhOR metapod metapone MetaProViz metaSeq metaseqR2 MetCirc methimpute methInheritSim methodical MethPed MethReg methrix MethTargetedNGS MethylAid methylCC methylclock methylGSA methyLImp2 methylInheritance methylKit MethylMix methylMnM methylPipe methylscaper MethylSeekR methylSig methylumi MetID MetMashR MetNet mfa Mfuzz MGFM MGFR MGnifyR mgsa mia miaDash miaSim miaTime miaViz MiChip microbiome microbiomeDASim microbiomeExplorer MicrobiomeProfiler MicrobiotaProcess microRNA microSTASIS MICSQTL midasHLA miloR mimager mina MineICA minet minfi MinimumDistance MiPP miQC MIRA MiRaGE miRBaseConverter miRcomp mirIntegrator MIRit miRLAB miRNAmeConverter miRNApath miRNAtap miRSM miRspongeR mirTarRnaSeq missMethyl missRows mist mistyR mitch mitoClone2 mitology mixOmics MLInterfaces MLP MLSeq MMDiff2 MMUPHin mnem moanin mobileRNA MODA ModCon Modstrings MOFA2 MOGAMUN mogsa MoleculeExperiment MOMA monaLisa monocle Moonlight2R MoonlightR mosaics mosbi MOSClip mosdef MOSim Motif2Site motifbreakR motifcounter MotifDb motifmatchr MotifPeeker motifStack motifTestR MouseFM MPAC MPFE mpra MPRAnalyze msa MSA2dist MsBackendMassbank MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendRawFileReader MsBackendSql MsCoreUtils MsDataHub MsExperiment MsFeatures msgbsR msImpute mslp msmsEDA msmsTests MSnbase MSnID mspms MSPrep msPurity msqrob2 MsQuality MSstats MSstatsBig MSstatsBioNet MSstatsConvert MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsQC MSstatsQCgui MSstatsResponse MSstatsShiny MSstatsTMT MuData Mulcom MultiAssayExperiment MultiBaC multiClust multicrispr MultiDataSet multiGSEA multiHiCcompare MultiMed multiMiR MultimodalExperiment MultiRNAflow multiscan multistateQTL multiWGCNA multtest mumosa MungeSumstats muscat muscle musicatk MutationalPatterns mutscan MutSeqR MVCClass MWASTools mygene myvariant mzID mzR NADfinder NanoMethViz NanoStringDiff NanoStringNCTools NanoTube NBAMSeq ncdfFlow ncGTW NCIgraph ncRNAtools ndexr nearBynding Nebulosa nempi NetActivity netboost nethet NetPathMiner netprioR netresponse NetSAM netSmooth netZooR NewWave ngsReports nipalsMCIA nnNorm nnSVG NOISeq nondetects NoRCE normalize450K NormalyzerDE NormqPCR normr notame notameStats notameViz NPARC npGSEA NTW nucleoSim nucleR nuCpos nullranges NuPoP OAtools occugene OCplus octad odseq OGRE oligo oligoClasses OLIN OLINgui omada OmaDB omicade4 OmicCircos omicplotR omicRexposome omicsGMF OmicsMLRepoR OMICsPCA omicsPrint omicsViewer Omixer OmnipathR ompBAM omXplore oncomix oncoscanR OncoScore OncoSimulR onlineFDR ontoProc openCyto openPrimeR OpenStats oposSOM oppar optimalFlow OPWeight OrderedList ORFhunteR ORFik Organism.dplyr OrganismDbi orthogene orthos OSAT Oscope OSTA.data OTUbase OUTRIDER OutSplice OVESEG PAA packFinder padma PADOG pageRank PAIRADISE paircompviz pairedGSEA pairkat pandaR panelcn.mops PanomiR panp PANR parati parglms parody partCNV PAST Path2PPI pathifier pathlinkR pathMED PathNet PathoStat pathRender pathview pathwayPCA pcaExplorer pcaMethods PCAN PCAtools PDATK pdInfoBuilder PeacoQC peakCombiner peakPantheR PECA peco Pedixplorer pengls PepSetTest PepsNMR pepStat pepXMLTab periodicDNA pfamAnalyzeR pgca pgxRpi phantasus phantasusLite PharmacoGx PhenoGeneRanker phenomis phenopath phenoTest philr PhIPData phosphonormalizer PhosR PhyloProfile phyloseq piano PICB pickgene Pigengene pipeComp pipeFrame PIPETS Pirat PIUMA plaid planet planttfhunter plasmut plgem plier PlinkMatrix plotgardener plotGrouper PLPE PLSDAbatch plyinteractions plyranges plyxp pmm pmp PMScanR PoDCall podkat poem pogos PolySTest Polytect POMA posDemux postNet powerTCR POWSC ppcseq PPInfer pqsfinder pram prebs preciseTAD PREDA preprocessCore primirTSS PrInCE proActiv proBAMr proBatch PROcess procoil proDA profileplyr profileScoreDist progeny projectR pRoloc pRolocGUI PROMISE PRONE PROPER PROPS Prostar proteinProfiles ProteoDisco ProteoMM protGear ProtGenerics psichomics PSMatch ptairMS PTMods puma PureCN pvac pvca Pviz pwalign PWMEnrich qcmetrics QDNAseq QFeatures qmtools qpcrNorm qpgraph qPLEXanalyzer QRscore qsea qsmooth QSutils qsvaR QTLExperiment Qtlizer quantiseqr quantro quantsmooth QuasR QuaternaryProd QUBIC queeems qusage qvalue R3CPET r3Cseq R453Plus1Toolbox R4RNA RadioGx raer RaggedExperiment RAIDS rain ramr ramwas randPack randRotation RankMap RankProd RAREsim RareVariantVis Rarr rawDiag rawrr RbcBook1 Rbec RBedMethyl RBGL RBioFormats rBiopaxParser rBLAST RBM Rbowtie Rbowtie2 RbowtieCuda rbsurv Rbwa RCAS RCASPAR rcellminer rCGH RcisTarget RCM Rcollectl Rcpi RCSL Rcwl RcwlPipelines RCX RCy3 RCyjs Rdisop RDRToolbox ReactomeGSA ReactomePA ReadqPCR REBET rebook receptLoss reconsi recount recount3 recountmethylation recoup RedeR RedisParam REDseq ReducedExperiment Rega RegEnrich regionalpcs RegionalST regioneR regioneReloaded regionReport regsplice regutools REMP ReportingTools RepViz ResidualMatrix RESOLVE retrofit ReUseData rexposome rfaRm Rfastp RFGeneRank RFLOMICS rfPred rGenomeTracks RgnTX rgoslin RGraph2js Rgraphviz rGREAT RGSEA rgsepd rhdf5 rhdf5client rhdf5filters Rhdf5lib rhinotypeR Rhisat2 Rhtslib RiboCrypt RiboDiPA RiboProfiling ribor riboSeqR ribosomeProfilingQC rifi rifiComparative Rigraphlib rigvf RImmPort RITAN RIVER RJMCMCNucleosomes RLassoCox RLMM Rmagpie RMassBank rmelting Rmmquant rmspc RNAAgeCalc RNAdecay rnaEditr RNAmodR RNAmodR.AlkAnilineSeq RNAmodR.ML RNAmodR.RiboMethSeq RNAsense rnaseqcomp RNAseqCovarImpute RNASeqPower RnaSeqSampleSize RNAshapeQC RnBeads Rnits roar roastgsa ROC ROCpAI RolDE rols ROntoTools ropls ROSeq ROTS RPA rprimer RProtoBufLib rpx Rqc rqt rqubic RRHO rrvgo Rsamtools rsbml rScudo rsemmed RSeqAn Rsubread RSVSim rSWeeP RTCA RTCGA RTCGAToolbox RTN RTNduals RTNsurvival RTopper Rtpca rtracklayer rTRM rTRMui RUCova runibic RUVcorr RUVnormalize RUVSeq Rvisdiff RVS rWikiPathways S4Arrays S4Vectors safe sagenhaft SAIGEgds sampleClassifier SamSPECTRAL sangeranalyseR sangerseqR SanityR SANTA sarks saseR satuRn SBGNview SBMLR SC3 scafari Scale4C ScaledMatrix SCAN.UPC scanMiR scanMiRApp scAnnotatR SCANVIS SCArray SCArray.sat scater scatterHatch scBFA SCBN scBubbletree scCB2 scClassify sccomp scConform scDataviz scDblFinder scDD scDDboost scde scDesign3 scDiagnostics scDotPlot scds scECODA SCFA scFeatureFilter scFeatures scGPS scGraphVerse schex scHiCcompare scHOT scider scifer scLANE scLang scmap scMerge scMET scmeth scMitoMut scMultiSim SCnorm scone Sconify SCOPE scoreInvHap scoup scp scPassport scPCA scPipe scQTLtools scran scrapper scReClassify scRecover screenCounter ScreenR scRepertoire scRNAseqApp scruff scry scShapes scTensor scTGIF scTHI scToppR scTreeViz scTypeEval scuttle scviR SDAMS seahtrue sechm segmenter segmentSeq selectKSigs SELEX SemDist semisup SEMPLR seq.hotSPOT seq2pathway SeqArray seqCAT seqcombo SeqGate SeqGSEA Seqinfo seqLogo seqPattern seqsetvis SeqSQC Seqtometry SeqVarTools SEraster sesame SETA SEtools sevenbridges sevenC sfi SGCP SGSeq SharedObject shiny.gosling shinybiocloader shinyDSP shinyepico shinyMethyl ShortRead SIAMCAT SICtools SigCheck sigFeature SigFuge siggenes sights signatureSearch signeR signifinder SigsPack sigsquared SIM SIMAT SimBu SIMD SimFFPE similaRpeak SIMLR simona simPIC simpleSeg simplifyEnrichment sincell singIST SingleCellAlleleExperiment SingleCellExperiment SingleCellSignalR singleCellTK SingleMoleculeFootprinting SingleR singscore SiPSiC sitadela Site2Target sitePath sizepower sketchR skewr slalom slingshot SLqPCR SMAD smartid SmartPhos SMITE smoothclust smoppix SMTrackR SNAGEE snapcount snifter snm SNPediaR SNPhood SNPRelate snpStats soGGi SomaticSignatures SOMNiBUS sosta SpaceMarkers SpaceTrooper spacexr Spaniel SpaNorm spARI sparrow SparseArray sparseMatrixStats sparsenetgls SparseSignatures spaSim SpatialArtifacts SpatialCPie spatialDE SpatialDecon SpatialExperiment SpatialExperimentIO spatialFDA SpatialFeatureExperiment spatialHeatmap SpatialOmicsOverlay spatialSimGP spatzie speckle specL SpeCond Spectra SpectralTAD SpectraQL SpectriPy SPEM SPIA SPIAT SPICEY spicyR SpiecEasi spikeLI spiky spillR spkTools splatter SpliceImpactR splicelogic SpliceWiz SplicingFactory SplicingGraphs SplineDV splineTimeR SPLINTER splots SpNeigh SPONGE spoon SpotClean SPOTlight SpotSweeper spqn SPsimSeq SQLDataFrame squallms sRACIPE SRAdb srnadiff sscu sSeq ssize sSNAPPY ssPATHS ssrch ssviz StabMap STADyUM stageR standR staRgate STATegRa StatescopeR Statial statTarget stepNorm stJoincount stPipe strandCheckR STRINGdb struct Structstrings structToolbox StructuralVariantAnnotation SubCellBarCode subSeq SUITOR SummarizedExperiment Summix SuperCellCyto supersigs surfaltr SurfR survClust survcomp survtype sva svaNUMT svaRetro SVMDO SVP SWATH2stats SwathXtend swfdr switchBox switchde synapsis synergyfinder SynExtend synlet SynMut syntenet systemPipeR systemPipeShiny systemPipeTools tadar TADCompare tanggle TAPseq target TargetDecoy TargetScore TargetSearch TaxSEA TBSignatureProfiler TCC TCGAbiolinks TCGAutils TCseq TDbasedUFE TDbasedUFEadv TEKRABber TENET TENxIO tenXplore TEQC terapadog ternarynet terraTCGAdata TFARM TFBSTools TFEA.ChIP TFHAZ TFutils tidybulk tidyCoverage tidyexposomics tidyFlowCore tidyomics tidyprint tidysbml tidySingleCellExperiment tidySpatialExperiment tidySummarizedExperiment tidytof tigre TileDBArray tilingArray timecourse timeOmics timescape TIN TissueEnrich tkWidgets tLOH TMixClust TMSig TnT TOAST tomoda tomoseqr TOP topconfects topdownr topGO toppgene ToxicoGx TPP TPP2D tpSVG tracktables trackViewer tradeSeq TrajectoryGeometry TrajectoryUtils transcriptogramer transcriptR transformGamPoi transite tRanslatome transmogR transomics2cytoscape traseR TreeAndLeaf treeclimbR treeio treekoR TreeSummarizedExperiment TREG Trendy TRESS tricycle TrIdent trio triplex tripr tRNA tRNAdbImport tRNAscanImport TRONCO TSAR TSCAN ttgsea TTMap TurboNorm TVTB tweeDEseq twilight twoddpcr txcutr txdbmaker tximeta tximport UCell UCSC.utils Ularcirc UMI4Cats uncoverappLib UNDO unifiedWMWqPCR UniProt.ws Uniquorn universalmotif updateObject UPDhmm uSORT VAExprs VanillaICE VarCon variancePartition VariantAnnotation VariantExperiment VariantFiltering VariantTools VaSP vbmp VCFArray VDJdive VegaMC velociraptor veloviz VennDetail VERSO vidger viper ViSEAGO VisiumIO visiumStitched vissE VISTA vmrseq Voyager VplotR vsclust vsn vtpnet vulcan waddR wateRmelon wavClusteR wavFeatExt weaver webbioc weitrix widgetTools wiggleplotr wpm wppi Wrench XAItest xCell2 xcms xcore XDE XeniumIO xenLite Xeva XINA xmapbridge XVector yamss YAPSA yarn ZarrArray zellkonverter zenith zFPKM zinbwave zitools ZygosityPredictor

AssayDomain (955)

BG2 cbaf CuratedAtlasQueryR GWAS.BAYES iGC MetID nondetects pgca ScreenR tidybulk tidyomics tidySingleCellExperiment tidySummarizedExperiment

aCGH (9)

ADaCGH2 biomvRCNS GeneBreak KCsmart mBPCR RCASPAR rcellminer rCGH VegaMC

ChIPchip (6)

ChIPpeakAnno ChIPXpress iChip les motifStack sevenC

CpGIsland (12)

bigmelon genomation HELP MAGAR MEDIPS MEDME methylumi planet PoDCall qsea RnBeads TurboNorm

DNAMethylation (114)

ARRmNormalization BEAT BEclear betaHMM bigmelon biscuiteer BiSeq borealis BPRMeth bsseq bumphunter cbaf cfTools ChAMP COCOA coMethDMR conumee CTexploreR DAMEfinder decemedip deconvR dmGsea DMRcaller DMRcate dmrseq DSS edgeR ELMER EnMCB ENmix epialleleR EpiDISH EpiMix epimutacions funtooNorm GAprediction GEM GeoTcgaData Harman HELP HIREewas hummingbird iCheck iNETgrate iscream knowYourCG les Lheuristic lumi MAGAR MassArray MBAmethyl mCSEA MEAL MEAT MEDIPS MEDME Melissa methimpute methInheritSim methodical MethPed methrix MethylAid methylCC methylclock methylGSA methyLImp2 methylInheritance methylKit MethylMix methylMnM methylPipe methylscaper MethylSeekR methylSig methylumi minfi MIRA missMethyl mist mitch Moonlight2R MoonlightR MPFE NanoMethViz normalize450K omicsPrint pathwayPCA planet PoDCall qsea ramr ramwas RBedMethyl recountmethylation regionalpcs REMP RnBeads RTCGA scMET scmeth sesame shinyepico shinyMethyl skewr SOMNiBUS spiky TCGAbiolinks TENET TOAST TurboNorm vmrseq wateRmelon

ExonArray (12)

AMARETTO asuri globalSeq limma oligo PECA puma regsplice roastgsa siggenes snm TIN

GeneExpression (635)

a4Classif acde ADAM ADImpute AffiXcan affycoretools affylmGUI AffyRNADegradation AGDEX aggregateBioVar AIMS airpart ALDEx2 AMARETTO AMOUNTAIN Anaquin anota anota2seq antiProfiles APAlyzer apeglm APL ASpli ASSIGN ASURAT asuri atena attract AUCell autonomics awst bambu BANDITS Banksy BASiCS BASiCStan batchelor BatchQC BayesKnockdown BayesSpace BgeeCall BgeeDB BindingSiteFinder biobroom bioCancer BioCor BiocSet BioNERO BioNet BioQC BioTIP biotmle blacksheepr blase blima BloodGen3Module bluster bnem BPRMeth BreastSubtypeR broadSeq BUMHMM BUScorrect BUSseq CaDrA CAEN CAFE CAGEfightR cageminer CAGEr calm canceR cardelino carnation CARNIVAL casper categoryCompare CatsCradle cbaf CBNplot CCPROMISE celda CelliD cellity CellMapper CellMixS CellTrails CEMiTool Cepo CeTF CHETAH chevreulPlot chevreulProcess chevreulShiny CiteFuse CleanUpRNAseq clustComp ClusterGVis ClusterJudge clusterSeq clustifyr clustSIGNAL cmapR CNVRanger CoGAPS cogena cola compEpiTools CONFESS consensus consensusOV Coralysis coRdon corral coseq CoSIA COTAN covEB covRNA CPSM crumblr csdR CSOA CTdata CTexploreR cTRAP ctsGE CTSV cummeRbund CuratedAtlasQueryR cypress cytoKernel damidBind DART dcGSA ddCt dearseq debrowser DeconvoBuddies deconvR decoupleR DeeDeeExperiment DeepTarget DEFormats DegCre DegNorm DEGreport DEGseq DELocal DeMAND DeMixT DenoIST DESeq2 DEsingle DESpace DEsubs DExMA DEXSeq diffcoexp DifferentialRegulation diffuStats diffUTR diggit Dino distinct dittoSeq dmGsea DMRcate dominatR doppelgangR doseR DOtools DOTSeq dreamlet DRIMSeq DropletUtils DrugVsDisease DSS DTA Dune easier EasyCellType easyRNASeq EBSEA edge edgeR eds EGSEA eisaR ELMER EMDomics EmpiricalBrownsMethod EnhancedVolcano EnrichmentBrowser epidecodeR epigenomix EpiMix epiregulon epiregulon.extra epistack erccdashboard ERSSA EWCE ExiMiR fastLiquidAssociation ffpe fgsea findIPs fishpond FLAMES gage gatom GDCRNATools gDNAx GEM gemma.R geneClassifiers GeneExpressionSignature genefu GeneGA GeneMeta GeneTonic GENIE3 genomicInstability GenomicOZone GenomicPlot GeoDiff GEOexplorer GeomxTools GeoTcgaData gep2pep getDEE2 geva geyser gg4way GGPA ggsc ggspavis GIGSEA gINTomics Glimma globalSeq GmicR GNET2 GOexpress GOpro goProfiles goseq goSorensen goSTAG GOstats GPA GRaNIE granulator GraphExperiment GRENITS GSABenchmark GSALightning GSCA GSEABase GSEABenchmarkeR gsean GSgalgoR GSReg GWENA hammers HDTD hipathia HIPPO HTqPCR HTSFilter hummingbird HVP HybridExpress HybridMTest iBMQ icetea iCheck ideal iGC ILoReg IMAS iModMix iNETgrate Informeasure InTAD IntramiRExploreR iPath iSEE iSEEfier iSEEpathways iSEEu ISLET IsoBayes IsoformSwitchAnalyzeR ISoLDE IVAS ivygapSE jazzPanda KBoost KEGGlincs kmcut KnowSeq leapR levi limma limmaGUI limpa limpca LimROTS Linnorm lionessR LiquidAssociation lncRna loci2path looking4clusters LRcell LRDE M3C M3Drop made4 markeR massiR MAST mastR MBASED mbkmeans MBttest MCbiclust MEB Melissa messina MetaNeighbor MetaPhOR metaseqR2 MethReg MethylMix mfa MGFM MGFR MICSQTL miQC MiRaGE MIRit miRLAB miRSM miRspongeR mitch mitology MLP mnem MODA mogsa monocle Moonlight2R MoonlightR mosdef MPRAnalyze Mulcom MultiBaC multiClust MultiRNAflow multistateQTL multiWGCNA NanoStringNCTools NanoTube NBAMSeq Nebulosa nempi NetActivity netresponse netSmooth netZooR NewWave nnSVG nondetects NormqPCR OAtools octad oligo omada omicplotR omicRexposome omicsGMF oncomix oposSOM oppar orthogene orthos Oscope OSTA.data OUTRIDER OutSplice OVESEG padma pairedGSEA pandaR PanomiR pathview pathwayPCA PCAtools PDATK PECA peco phantasus phantasusLite PharmacoGx phenopath piano Pigengene pipeComp plaid plgem postNet ppcseq prebs PREDA proActiv progeny PROMISE PROPS psichomics puma qpcrNorm qpgraph QRscore quantiseqr QuaternaryProd QUBIC R3CPET randRotation RankMap RankProd RCASPAR rcellminer ReactomeGSA ReadqPCR receptLoss recount recount3 recoup ReducedExperiment RegEnrich regutools retrofit RFGeneRank RiboDiPA RIVER RLassoCox Rmmquant RNAAgeCalc RNAdecay RNAsense RNAseqCovarImpute RnaSeqSampleSize Rnits roastgsa ROSeq ROTS RPA rScudo Rsubread RTCGAToolbox RTN RTNduals RUVcorr sampleClassifier SanityR sarks saseR satuRn SBGNview scAnnotatR scater scBFA SCBN scCB2 scClassify scDataviz scDDboost scDesign3 scDiagnostics scDotPlot scds scFeatureFilter scHOT scLANE scLang scmap scMerge scMET scMultiSim scone scp scPCA scPipe scQTLtools scran scrapper ScreenR scry scShapes scTensor scTGIF scTypeEval scuttle sechm SeqGate SeqGSEA Seqtometry SEraster SETA SEtools SGCP shinyDSP SigCheck sigFeature siggenes signatureSearch signifinder SIMLR sincell SingleCellAlleleExperiment singleCellTK SingleR singscore Site2Target slalom slingshot smartid SmartPhos smoothclust snapcount snm SpaceMarkers SpaceTrooper spacexr Spaniel SpaNorm spARI SpatialDecon SpatialExperiment SpatialExperimentIO spatialHeatmap SpatialOmicsOverlay spatialSimGP speckle SPICEY splatter SplicingGraphs SplineDV splineTimeR SPLINTER SpNeigh SPONGE spoon SpotClean SpotSweeper SPsimSeq sRACIPE srnadiff sscu sSNAPPY ssPATHS standR StatescopeR stPipe subSeq SurfR survcomp survtype SVP switchde systemPipeR TBSignatureProfiler TCGAbiolinks TDbasedUFE TDbasedUFEadv TEKRABber TENET TFEA.ChIP tidybulk tidyexposomics tidyomics tidySingleCellExperiment tidySpatialExperiment tidySummarizedExperiment tigre TIN TissueEnrich tLOH TMixClust TOAST tomoda tomoseqr TOP topconfects topGO toppgene ToxicoGx tpSVG tradeSeq TrajectoryGeometry TrajectoryUtils transcriptogramer transite tRanslatome TREG tripr TSCAN ttgsea tximeta tximport UCell unifiedWMWqPCR VAExprs variancePartition velociraptor veloviz vidger viper visiumStitched vissE VISTA Voyager vulcan weitrix wiggleplotr xCell2 xcore Xeva yarn zenith zFPKM zinbwave

Transcription (185)

AffiXcan affylmGUI aggregateBioVar airpart altcdfenvs AMARETTO annmap ASpli atena AUCell autonomics bambu BANDITS BicARE BiFET BioTIP blacksheepr blase BUMHMM CAGEfightR CAGEr carnation casper cbaf CeTF chevreulPlot chevreulProcess chevreulShiny ChIPanalyser ChIPexoQual CoGAPS consensusSeekeR covRNA CSAR ctsGE CuratedAtlasQueryR customProDB damidBind dearseq decoupleR DeeDeeExperiment DEFormats DepecheR DESeq2 diffcoexp DifferentialRegulation dinoR distinct DTA easier edgeR eisaR ELMER EnhancedVolcano epidecodeR epiregulon epiregulon.extra epiRomics erccdashboard ERSSA EventPointer EWCE ExiMiR fCCAC fishpond gDNAx GeDi GeneTonic GenomicOZone GenomicPlot GeomxTools gg4way GOexpress goseq GRaNIE GSALightning GSgalgoR GSRI Guitar Harman icetea ILoReg IMAS InPAS iSEE iSEEfier iSEEu ISLET IsoformSwitchAnalyzeR ISoLDE IVAS ivygapSE KBoost knowYourCG les limma Linnorm lncRna M3C MBASED MBttest metaseqR2 methodical MethReg mosaics mosdef motifbreakR motifcounter MultiBaC MultiRNAflow NanoStringNCTools NetActivity netresponse netZooR OMICsPCA omicsPrint pairedGSEA pandaR pathwayPCA PCAtools PIPETS planttfhunter ppcseq primirTSS proActiv psichomics qpgraph quantiseqr QuaternaryProd RcisTarget RegEnrich regionReport regutools RgnTX RIVER Rmmquant RNAdecay roar roastgsa RRHO RTN rTRM rTRMui SC3 scDataviz scde scDotPlot scmap SELEX SEMPLR SGSeq sigFeature SiPSiC sitadela snm SpatialOmicsOverlay spatzie SPICEY SplicingGraphs SPONGE STADyUM subSeq SurfR SVP target TEKRABber TENET TFARM TFBSTools TFEA.ChIP TFHAZ tidybulk tidyomics tidySummarizedExperiment tigre tLOH transcriptogramer transcriptR transite TREG tricycle tximeta tximport visiumStitched wiggleplotr

Technology (1587)

ACME amplican BioGA CIMICE compSPOT consICA CoverageView DMRScan dupRadar HiCBricks IFAA iGC LymphoSeq MDTS metapone MetID MPAC nondetects openPrimeR optimalFlow ORFhunteR pram scruff seq.hotSPOT spkTools TAPseq wavClusteR

Sequencing (920)

abseqR ACE ADAPT ADImpute airpart ALDEx2 AllelicImbalance AMARETTO ANCOMBC AnnotationDbi anota anota2seq APAlyzer apeglm APL appreci8R ASpli ASURAT atacInferCnv ATACseqQC ATACseqTFEA atena awst BaalChIP BADER BadRegionFinder bambu bamsignals BANDITS barbieQ barcodetrackR basecallQC BaseSpaceR Basic4Cseq BASiCS BASiCStan BatChef batchelor BatchQC Battlefield bayNorm baySeq BBCAnalyzer bcSeq beer betaHMM betterChromVAR BgeeDB BindingSiteFinder biomvRCNS Biostrings BioTIP biotmle BiSeq blacksheepr blase borealis BPRMeth breakpointR broadSeq BSgenomeForge BubbleTree BUMHMM BUSseq CAEN CAGEfightR CAGEr calm cardelino casper ccImpute CDI celda CellBarcode cellity CellTrails Cepo CeTF CexoR cfdnakit cfDNAPro cfTools chevreulPlot chevreulProcess chevreulShiny Chicago ChIPanalyser ChIPexoQual ChIPQC chipseq chromPlot chromVAR cicero cigarillo CircSeqAlignTk cleanUpdTSeq CleanUpRNAseq cliProfiler Clomial ClonalSim clstutils clusterExperiment clusterSeq clustifyr cn.mops CNAnorm CNVfilteR CNViz CNVPanelizer CNVrd2 COCOA cogena Cogito compEpiTools ComplexHeatmap compSPOT condiments consensusSeekeR consICA CopyNumberPlots corral coseq CoverageView CrispRVariants csaw CSSQ ctsGE CuratedAtlasQueryR customProDB cypress dada2 damidBind DaMiRseq dar dcGSA dearseq debrowser decemedip DECIPHER decompTumor2Sig decontam deepSNV DEFormats DegNorm DeMixT demuxmix densvis derfinder derfinderHelper derfinderPlot DEScan2 DESeq2 DEsingle DESpace DEWSeq DEXSeq DiffBind diffcoexp DifferentialRegulation diffHic Dino dinoR DirichletMultinomial distinct DMCFB DMCHMM dmGsea DMRcaller DMRcate DMRScan dmrseq DNABarcodeCompatibility DNABarcodes DNAfusion doseR DOTSeq dreamlet DRIMSeq DropletUtils DspikeIn DSS dStruct DuplexDiscovereR dupRadar easylift EBSEA EBSeq EDASeq edgeR eds EGSEA ELViS enhancerHomologSearch EnrichedHeatmap ensembldb epiRomics esATAC escape EventPointer extraChIPs FastqCleaner fastRanges fCCAC FEAST FilterFFPE fishpond fourSynergy fRagmentomics fraq FRASER gage GBScleanR gcapc gDNAx GDSArray GeneBreak GeneMeta GeneNetworkBuilder geneRxCluster genomation GenomicAlignments GenomicDataCommons GenomicDistributions GenomicFeatures GenomicFiles GenomicInteractionNodes GenomicOZone GenomicPlot GenomicRanges GenomicScores GenomicSuperSignature GenomicTuples GeomxTools getDEE2 gg4way Glimma globalSeq GloScope gmoviz GMRP GOexpress goseq GOTHiC GreyListChIP groHMM gtrellis GUIDEseq Guitar gVenn Gviz GWENA hapFabia HDF5Array HDTD HelloRanges HiCaptuRe HiCBricks HiCcompare HiCDOC HilbertCurve HiLDA HIPPO HiTC HMMcopy HTSFilter hummingbird Ibex icetea ideal IFAA iGC igvShiny IMAS immApex immLynx immReferent INSPEcT InTAD intansv InteractiveComplexHeatmap IntEREst IONiseR ISAnalytics iscream iSeq ISLET IsoBayes ISoLDE IVAS ivygapSE karyoploteR katdetectr KnowSeq knowYourCG LACHESIS LedPred lefser levi limma lineagespot linkSet Linnorm loci2path LOLA LRcell LRDE LymphoSeq M3C M3Drop m6Aboost Macarron made4 maftools MAGAR magpie MBASED mbkmeans MBttest MDTS MEB MEDIPS Melissa metabinR MetaDICT metagene2 metagenomeSeq MetaPhOR metaSeq metaseqR2 methimpute methInheritSim methrix MethTargetedNGS methylCC methylInheritance methylKit methylMnM methylPipe methylscaper MethylSeekR miaSim miaTime microbiome microbiomeExplorer MICSQTL miQC MIRA MiRaGE miRNAtap mirTarRnaSeq mixOmics MLSeq MMDiff2 mobileRNA Modstrings monocle mosaics Motif2Site motifStack MPAC mpra MPRAnalyze msa MSA2dist multiHiCcompare MultiRNAflow multistateQTL multiWGCNA muscat muscle MutSeqR NADfinder NBAMSeq netSmooth NewWave NOISeq nucleoSim nucleR OGRE omicplotR omicsGMF ompBAM oncomix ORFhunteR ORFik Organism.dplyr Oscope OTUbase OUTRIDER panelcn.mops parati PathoStat pathview PCAN peco periodicDNA phenomis philr PhIPData phyloseq PICB PIPETS planttfhunter plasmut podkat posDemux postNet ppcseq pram prebs preciseTAD primirTSS profileplyr PROPER ProteoDisco psichomics PureCN pwalign QDNAseq qsea qsmooth QSutils qsvaR QTLExperiment quantiseqr quantro QuasR queeems r3Cseq R453Plus1Toolbox raer RAIDS ramwas randRotation RAREsim RareVariantVis Rbec rBLAST Rbowtie Rbowtie2 Rbwa RCSL recount recount3 recoup REDseq regionReport regsplice REMP RepViz Rfastp RgnTX rGREAT rhinotypeR Rhisat2 Rhtslib RiboCrypt RiboDiPA RiboProfiling riboSeqR ribosomeProfilingQC RJMCMCNucleosomes rmspc RNAmodR RNAmodR.AlkAnilineSeq RNAmodR.ML RNAmodR.RiboMethSeq RNAseqCovarImpute RnaSeqSampleSize RNAshapeQC RnBeads roar roastgsa Rqc rqt Rsamtools Rsubread RSVSim RTCGAToolbox sangeranalyseR sangerseqR saseR satuRn SBGNview scafari Scale4C scater scCB2 scDDboost scDesign3 scDotPlot scds scGPS scGraphVerse schex scHiCcompare scHOT scifer scLANE scmap scMerge scMET scMitoMut scMultiSim scone SCOPE scoup scPCA scPipe scran scRepertoire scruff scry scuttle segmentSeq selectKSigs seq.hotSPOT SeqArray seqCAT SeqGate SeqGSEA seqsetvis SeqVarTools ShortRead SIAMCAT SICtools signatureSearch SimFFPE SIMLR simPIC sincell SiPSiC sitadela slalom slingshot SMITE snapcount snifter soGGi SomaticSignatures SOMNiBUS Spaniel spatialHeatmap SpectralTAD spiky splatter SpliceWiz SplicingGraphs SplineDV splots SpotClean SPsimSeq SRAdb ssviz STADyUM stPipe Structstrings StructuralVariantAnnotation subSeq SummarizedExperiment supersigs SurfR survtype sva svaNUMT svaRetro systemPipeR systemPipeShiny systemPipeTools tadar TADCompare TAPseq TaxSEA TCC TCGAbiolinks TCseq TENET TEQC TFEA.ChIP tidybulk tidyCoverage tidyomics tidySingleCellExperiment tidySpatialExperiment tidySummarizedExperiment timeOmics TissueEnrich tomoda tomoseqr topGO tracktables tradeSeq transcriptR transmogR traseR TREG TrIdent TVTB tweeDEseq txcutr txdbmaker Ularcirc UMI4Cats VariantAnnotation VariantExperiment VariantFiltering VariantTools VCFArray velociraptor veloviz VERSO vmrseq VplotR wavClusteR wiggleplotr Wrench xcore YAPSA yarn zinbwave

DNaseSeq (9)

BiFET COCOA DegCre DiffBind EpiCompare epigraHMM esATAC HicAggR nullranges

RiboSeq (10)

DOTSeq ORFik postNet RiboCrypt RiboDiPA RiboProfiling riboSeqR ribosomeProfilingQC systemPipeR terapadog

RNASeq (418)

aggregateBioVar AIMS airpart ALDEx2 AMARETTO Anaquin anota2seq APAlyzer apeglm APL ASpli atena attract autonomics awst bacon BADER ballgown bambu BANDITS Basic4Cseq BASiCS BASiCStan batchelor BatchQC bayNorm BgeeCall BioTIP biotmle blacksheepr blase BPRMeth BreastSubtypeR broadSeq BulkSignalR BUMHMM BUSpaRse CaDrA CAEN calm cardelino casper CausalR ccImpute CDI CelliD cellity CEMiTool CeTF CHETAH chevreulPlot chevreulProcess chevreulShiny clusterExperiment ClusterFoldSimilarity ClusterGVis CNVRanger CoGAPS compcodeR condiments CONFESS consensus consICA Coralysis coseq countsimQC covEB CoverageView cqn crumblr cTRAP ctsGE CuratedAtlasQueryR customProDB cypress DaMiRseq dcGSA dearseq debrowser DeconvoBuddies deconvR DeepTarget DEFormats DegCre DegNorm DEGreport DEGseq DELocal DepecheR derfinder derfinderHelper derfinderPlot DESeq2 DEsingle DESpace DEsubs DEXSeq diffcoexp DifferentialRegulation Dino discordant distinct dittoSeq doppelgangR DOtools DOTSeq dreamlet DRIMSeq DropletUtils DSS Dune dupRadar easyRNASeq EBSeq EDASeq edgeR eds EGSEA eisaR EnhancedVolcano EnrichmentBrowser epiRomics epistack erccdashboard ERSSA EventPointer EWCE ExCluster fCCAC fishpond FLAMES FRASER gage gCrisprTools GDCRNATools gDNAx GeDi GeneStructureTools GenomicAlignments GenomicOZone GenomicPlot GenomicSuperSignature GEOexplorer GEOfastq GeomxTools GeoTcgaData geva gg4way gINTomics Glimma glmGamPoi globalSeq GloScope GOexpress goseq goSTAG GRaNIE granulator GSEABenchmarkeR GSVA Guitar GWENA HDF5Array hermes HGC HicAggR HTSFilter HybridExpress iASeq iasva icetea ideal IHW ILoReg IMAS iNETgrate INSPEcT InTAD IntEREst ISLET IsoBayes IsoformSwitchAnalyzeR ISoLDE isomiRs IVAS kissDE KnowSeq limma LimROTS Linnorm lncRna LRDE M3C M3Drop magpie marr MAST mbkmeans MCbiclust megadepth Melissa MetaPhOR metaSeq metaseqR2 mfa MGFR MICSQTL MiRaGE miRspongeR mitology MLSeq mnem mobileRNA monocle MOSim MPAC MultiRNAflow multiWGCNA mumosa NanoStringNCTools NBAMSeq nempi NetActivity netSmooth NOISeq nullranges omada omicplotR omicsGMF ompBAM OPWeight ORFhunteR ORFik orthos Oscope OUTRIDER OutSplice padma PAIRADISE pairedGSEA pathlinkR PathoStat pathview pcaExplorer PCAtools peco phantasus phantasusLite phenopath Pigengene poem POMA posDemux postNet ppcseq pram prebs primirTSS proActiv PROPER ProteoDisco psichomics qsmooth QuasR qusage raer randRotation RCSL RcwlPipelines recount recount3 recoup RegEnrich regionReport regsplice ReportingTools retrofit RFGeneRank RgnTX rgsepd RiboCrypt RiboDiPA rifi rifiComparative rmspc RNAAgeCalc RNAdecay rnaEditr RNAsense rnaseqcomp RNAseqCovarImpute RNASeqPower RnaSeqSampleSize RNAshapeQC roastgsa ROTS Rsubread RTCGA RUVSeq Rvisdiff sampleClassifier sarks saseR satuRn SBGNview SC3 SCAN.UPC SCArray SCArray.sat scater scBubbletree scCB2 scDataviz scDblFinder scDD scde scDiagnostics scDotPlot scds scFeatureFilter scGraphVerse scHOT scLANE scmap scMerge SCnorm scone scPCA scPipe scran scrapper scRNAseqApp scruff scry scShapes scuttle SeqGate SeqGSEA SETA SGCP SGSeq SigFuge signifinder SimBu sincell SingleCellSignalR SiPSiC sitadela slalom slingshot SMITE snapcount spacexr Spaniel SpatialCPie SpatialOmicsOverlay speckle splatter splicelogic SpliceWiz SplicingFactory SplicingGraphs SplineDV SPLINTER SpotClean SPsimSeq sSeq ssPATHS ssviz StatescopeR stPipe strandCheckR subSeq SurfR sva SVMDO switchde systemPipeR tadar TaxSEA TCC TCseq TENET TFEA.ChIP tidybulk tidyomics tidySingleCellExperiment tidySpatialExperiment tidySummarizedExperiment tomoda tomoseqr topconfects tradeSeq transcriptogramer transcriptR TREG Trendy TRESS tricycle tweeDEseq txcutr tximeta tximport uSORT variancePartition VaSP VDJdive veloviz vidger VISTA wavClusteR weitrix wiggleplotr xCell2 XINA zenith zFPKM zinbwave

RIPSeq (5)

BiFET CAEN DiffBind normr wavClusteR

ExomeSeq (7)

cardelino Clomial CODEX globalSeq iCNV RVS Uniquorn

miRNA (13)

globalSeq isomiRs miRBaseConverter miRLAB miRNAmeConverter miRNApath miRNAtap mirTarRnaSeq PanomiR rcellminer scanMiR scanMiRApp TargetScore

SangerSeq (3)

FastqCleaner sangeranalyseR scifer

SmallRNA (4)

CircSeqAlignTk mirTarRnaSeq mobileRNA srnadiff

DenovoGenome

TargetedResequencing (6)

Clomial DNAfusion LymphoSeq MDTS tripr VDJdive

DenovoTranscriptome

MicrobialStrain (1)

Rbec

PooledScreens (6)

gCrisprTools gscreend mnem nempi pogos TAPseq

MNaseSeq (2)

ATACseqTFEA fCCAC

LongRead (7)

bambu epialleleR FLAMES LRDE NanoMethViz splicelogic tximeta

Microarray (393)

a4 a4Base a4Classif a4Core a4Preproc a4Reporting ABarray acde ACME ADaCGH2 ADAM adSplit affxparser affy affycomp affycoretools affyILM affyio affylmGUI affyPLM AffyRNADegradation AGDEX AgiMicroRna AIMS altcdfenvs AMARETTO AMOUNTAIN annaffy annmap AnnotationDbi annotationTools anota anota2seq aroma.light ArrayExpress arrayMvout arrayQuality arrayQualityMetrics ARRmNormalization asuri attract autonomics BatchQC beadarray BeadDataPackR betaHMM BgeeDB BicARE bigmelon biomvRCNS BioNet biotmle blima BLMA CaDrA CAFE calm cancerclass CausalR cbaf CCPROMISE CellMapper CeTF CGHbase CGHcall cghMCR CGHnormaliter CGHregions ChAMP chopsticks clustifyr cn.farms CNTools CNVRanger codelink CoGAPS cogena coGPS consensus consensusOV conumee convert Cormotif covEB crlmm ctc cycle daMA dcGSA DECIPHER DEGraph DeMixT DFP diffcoexp diffGeneAnalysis discordant DMRcate DNAcopy doppelgangR DrugVsDisease DTA dyebias EGSEA EMDomics ENmix EnrichmentBrowser erccdashboard EWCE ExiMiR fabia factDesign fdrame ffpe flowVS frma frmaTools gage gcrma gemma.R genArise geneClassifiers genefilter GeneMeta GeneNetworkBuilder geneRecommender GeneRegionScan geNetClassifier GEOexplorer GEOquery GEOsubmission GeoTcgaData geva gINTomics GLAD Glimma GlobalAncova globaltest GOexpress goProfiles goSorensen goSTAG GOstats goTools gpls GSEABenchmarkeR GSEAlm GSRI GSVA Gviz GWASTools GWENA Harman HDTD Heatplus HELP HEM HERON HMMcopy HybridMTest iBMQ iCheck iChip IdeoViz iGC illuminaio impute IntramiRExploreR ITALICS iterativeBMA iterativeBMAsurv KCsmart KnowSeq les limma limmaGUI LimROTS lmdme LPE lumi maCorrPlot made4 MAGAR MANOR maPredictDSC marray maSigPro maskBAD massiR matchBox MBCB mBPCR MCbiclust mCSEA mdp mdqc MEAL MEAT MEDIPS MEDME MetaPhOR MethylAid methylCC methyLImp2 Mfuzz MGFM MiChip mimager minet minfi MinimumDistance MiPP MiRaGE mirIntegrator miRNAtap miRSM miRspongeR mixOmics MODA motifStack Mulcom multiscan multtest NetActivity netresponse netZooR nnNorm normalize450K npGSEA nucleR OCplus oligo OLIN OLINgui oncoscanR OrderedList PAA PADOG pandaR PathoStat pathview PECA pepStat phantasus phenoTest piano pickgene Pigengene planet plgem PLPE prebs PROMISE protGear puma pvac pvca Pviz qcmetrics qpgraph qsmooth quantiseqr quantro QUBIC qusage rain randRotation RankProd RBM rbsurv RDRToolbox recountmethylation regsplice REMP ReportingTools rifi rifiComparative RLMM Rmagpie Rnits roastgsa ROntoTools ROTS RPA RRHO RTopper sampleClassifier SBGNview SCAN.UPC scPCA semisup shinyepico shinyMethyl sigFeature siggenes signifinder SIM sizepower SNAGEE snm snpStats spatialHeatmap SpeCond SPIA spikeLI spkTools ssize stepNorm sva TEQC tigre tilingArray timecourse timeOmics TIN TOAST topGO transcriptogramer transite tRanslatome trio TTMap TurboNorm twilight variancePartition vsn wateRmelon webbioc xCell2 XDE zenith

MultiChannel (7)

aroma.light cytoviewer ENmix minfi Polytect REMP snm

GenotypingArray (2)

GDSArray VariantExperiment

MicroRNAArray (5)

AMARETTO GEOexplorer limma randRotation roastgsa

ChipOnChip (11)

ChIPanalyser epidecodeR epiregulon.extra motifTestR peakCombiner profileplyr puma qsea recoup rmspc TFEA.ChIP

ReversePhaseProteinArray

TissueMicroarray (2)

DeMixT spatialHeatmap

ProprietaryPlatforms (11)

affxparser affylmGUI altcdfenvs AMARETTO GeomxTools illuminaio limma metaseqR2 NanoStringNCTools roastgsa SpatialOmicsOverlay

MassSpectrometry (152)

Aerith AHMassBank apComplex artMS autonomics AWAggregator bandle batchCorr biosigner BRAIN CalibraCurve CAMERA Cardinal CardinalIO CATALYST Chromatograms cliqueMS CompoundDb ComPrAn CONSTANd cosmiq customProDB DAPAR DEqMS Doscheda FeatSeekR flagme fobitools gaga glycoTraitR hdxmsqc INDEED IPO isobar IsoBayes IsoCorrectoR IsoCorrectoRGUI koinar lcmsPlot limpa lipidr LOBSTAHS MAIT marr MassArray MassSpecWavelet metabCombiner MetaboAnnotation MetaboAnnotatoR MetaboCoreUtils metabomxtr metaMS metapone MetCirc MetNet MsBackendMassbank MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendRawFileReader MsBackendSql MsCoreUtils MsDataHub MsExperiment MsFeatures msImpute msmsEDA msmsTests MSnbase MSnID mspms MSPrep msPurity msqrob2 MsQuality MSstats MSstatsBig MSstatsBioNet MSstatsConvert MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsQC MSstatsQCgui MSstatsResponse MSstatsShiny MSstatsTMT mzID mzR ncGTW notame notameStats notameViz omicsGMF omXplore peakPantheR PepSetTest pepXMLTab pgca phenomis Pirat plgem pmp PolySTest proBAMr proBatch PROcess proDA pRoloc Prostar ProteoMM ProtGenerics PSMatch ptairMS PTMods qcmetrics QFeatures qmtools qPLEXanalyzer rawDiag rawrr Rdisop rgoslin RMassBank rols ropls rpx scDataviz scp SDAMS sfi SIMAT SMAD SmartPhos sparsenetgls specL Spectra SpectraQL SpectriPy spillR squallms statTarget SubCellBarCode SWATH2stats TargetDecoy TargetSearch topdownr TPP treekoR wpm xcms yamss

ImagingMassSpectrometry (2)

Cardinal CardinalIO

qPCR (13)

amplican ddCt DECIPHER HTqPCR miRcomp nondetects NormqPCR OAtools ReadqPCR rprimer SLqPCR TSAR unifiedWMWqPCR

MicrotitrePlateAssay (14)

bioassayR ChemmineOB ChemmineR ddCt eiR fmcsR HTqPCR NormqPCR ReadqPCR seahtrue sights SLqPCR splots unifiedWMWqPCR

SAGE (7)

BADER baySeq edgeR GEOquery MBttest MiRaGE sagenhaft

SingleCell (346)

ADImpute adverSCarial aggregateBioVar airpart alevinQC anglemania anndataR APL assorthead ASURAT atacInferCnv AUCell awst Banksy BASiCS BASiCStan BatChef batchelor BayesSpace bayNorm blase bluster BPRMeth breakpointR BUSpaRse BUSseq CAEN cardelino CARDspa CATALYST CatsCradle ccfindR ccImpute CCPlotR CDI celaref celda CellBench CelliD CellMentor cellmig CellMixS CellTrails cellxgenedp censcyt Cepo CeTF CHETAH chevreulPlot chevreulProcess chevreulShiny ChromSCape chromVAR cicero CIMICE CiteFuse clusterExperiment ClusterFoldSimilarity ClusterGVis clustifyr ClustIRR clustSIGNAL comapr compSPOT concordexR condiments Coralysis corral COTAN countsimQC crumblr CSOA cydar CyTOFpower cytofQC CytoGLMM cytoKernel cytomapper cytoMEM cytoviewer dandelionR DCATS decontX DeconvoBuddies deconvR demuxmix demuxSNP DenoIST densvis DepecheR DEsingle DESpace diffcyt DifferentialRegulation Dino distinct dittoSeq dominoSignal DOtools DOTSeq dreamlet DropletUtils drugfindR Dune EasyCellType edgeR eds epiregulon escape escheR EWCE FEAST fishpond FLAMES flowSpecs FuseSOM gemma.R genomicInstability gg4way ggsc ggspavis glmGamPoi GloScope granulator GraphExperiment GSABenchmark hammers hca HDF5Array HGC HIPPO hoodscanR HuBMAPR HVP Ibex ILoReg imcRtools immApex immLynx immunoClust infercnv infinityFlow InterCellar ISAnalytics iscream iSEE iSEEfier iSEEhub iSEEu jvecfor knowYourCG LACE lemur linkSet Linnorm lisaClust LoomExperiment LRcell MAPFX MAST mbkmeans Melissa MetaNeighbor methylscaper mfa MICSQTL miloR miQC miRspongeR mist mistyR mitch mitoClone2 mitology mnem MultimodalExperiment mumosa muscat Nebulosa nempi netSmooth NewWave nipalsMCIA nnSVG omicsGMF OMICsPCA OmnipathR ompBAM OSTA.data partCNV PCAtools peco phenopath poem POWSC raer RankMap RCSL retrofit ROSeq Rsubread RUCova SanityR satuRn SC3 scafari scAnnotatR SCArray SCArray.sat scater scatterHatch scBFA scBubbletree scCB2 scClassify sccomp scConform scDataviz scDblFinder scDD scDDboost scDesign3 scDiagnostics scDotPlot scds scECODA scFeatureFilter scFeatures scGPS scGraphVerse schex scHiCcompare scHOT scifer scLANE scLang scmap scMerge scMET scmeth scMitoMut scMultiSim SCnorm scone Sconify SCOPE scp scPassport scPipe scQTLtools scran scrapper scReClassify scRepertoire scRNAseqApp scruff scry scShapes scTensor scTGIF scTHI scToppR scTreeViz scTypeEval scuttle scviR SDAMS Seqtometry SEraster SETA signifinder SimBu SIMD SIMLR simPIC simpleSeg singIST SingleCellAlleleExperiment SingleCellExperiment SingleCellSignalR singleCellTK SingleR SiPSiC sketchR slalom slingshot smoothclust smoppix snifter SpaceMarkers SpaceTrooper spacexr Spaniel SpatialExperiment SpatialExperimentIO spatialHeatmap speckle SPIAT SPICEY spicyR spillR splatter SplineDV SpNeigh spoon SpotClean SPOTlight SPsimSeq StabMap StatescopeR Statial stPipe SuperCellCyto SVP switchde synapsis TAPseq TDbasedUFE TDbasedUFEadv TENxIO tenXplore tidyFlowCore tidySingleCellExperiment tidySpatialExperiment tidytof tradeSeq TrajectoryGeometry TrajectoryUtils transformGamPoi treekoR TREG tricycle TRONCO tximeta UCell VAExprs VDJdive velociraptor VisiumIO vmrseq waddR weitrix xCell2 XeniumIO zellkonverter zinbwave

ddPCR (5)

ddPCRclust PoDCall Polytect rprimer twoddpcr

AnnotationHubSoftware (4)

AHMassBank customCMPdb GenomicScores ipdDb

ExperimentHubSoftware (11)

CTdata CTexploreR DeconvoBuddies DEqMS easier hpar m6Aboost MsDataHub OSTA.data quantiseqr standR

ResearchField (1180)

cbaf CIMICE iGC INDEED MethTargetedNGS MetID PhosR pram queeems RankProd SCANVIS scoup sRACIPE

Genetics (208)

aCGH AGDEX AllelicImbalance AlphaBeta ASAFE AssessORF BANDITS BaseSpaceR BEAT BiFET biomvRCNS Biostrings BiSeq BPRMeth BSgenome BUMHMM calm cbaf CCAFE chromPlot cliProfiler Clomial cn.mops comapr consensusSeekeR CONSTANd cpvSNP CSAR csaw ctsGE CTSV dearseq DECIPHER decompTumor2Sig deepSNV DifferentialRegulation diffuStats discordant distinct DMRcate DNAfusion DOTSeq DRIMSeq easyRNASeq edgeR EDIRquery EGSEA ensembldb EpiCompare epistasisGA erccdashboard EWCE FamAgg fastLiquidAssociation fRagmentomics FRASER frenchFISH FRGEpistasis gage GBScleanR gCrisprTools GeneBreak geneplast geneRxCluster GENESIS GeneticsPed GenomeInfoDb genomeIntervals genomes GenomicAlignments GenomicFeatures GenomicFiles GenomicOZone GenomicRanges GenomicScores GEWIST ggmanh GGPA ginmappeR goatea GPA GrafGen GRaNIE gwascat gwasurvivr hapFabia HDTD HIBAG HybridMTest iGC IgGeneUsage immunotation infercnv intansv IsoBayes ISoLDE KnowSeq limma Linnorm LiquidAssociation loci2path logicFS m6Aboost martini MassArray MatrixRider mCSEA MEDIPS Melissa metaCCA metagene2 MethTargetedNGS MGFM MGFR MICSQTL midasHLA mitoClone2 MLP mosaics MotifPeeker MouseFM MSA2dist MungeSumstats muscle MutationalPatterns netresponse normr nucleoSim nucleR nuCpos NuPoP OmaDB omicsPrint orthogene OUTRIDER packFinder panelcn.mops parati pathview pathwayPCA PCAN Pedixplorer PICB PIPETS PlinkMatrix podkat PREDA primirTSS pwalign QDNAseq qpgraph QSutils Qtlizer QuasR queeems RAIDS rain randRotation RAREsim rBLAST RCASPAR regioneR regioneReloaded rhinotypeR riboSeqR RIVER RRHO Rsubread RVS SAIGEgds sangeranalyseR SBGNview scMET scoreInvHap scoup scQTLtools semisup SeqArray SeqVarTools shiny.gosling similaRpeak SingleCellAlleleExperiment SNPRelate SplicingGraphs sscu ssviz StructuralVariantAnnotation SUITOR SummarizedExperiment Summix svaNUMT svaRetro SynExtend systemPipeR TENET TEQC TIN toppgene transite traseR trio TVTB txdbmaker Ularcirc UPDhmm VariantAnnotation VariantFiltering VariantTools

Metabolomics (123)

Aerith AlpsNMR anansi ASICS autonomics batchCorr bioassayR biosigner BridgeDbR CalibraCurve calm CAMERA ChemmineOB ChemmineR Chromatograms cliqueMS CluMSID combi CompoundDb cosmiq cosmosR diffuStats DNEA drugTargetInteractions EGSEA eiR ExpoRiskR FELLA fmcsR fobitools funOmics graphite hdxmsqc hmdbQuery iModMix INDEED IPO IsoCorrectoR IsoCorrectoRGUI lcmsPlot limma limpca LimROTS LOBSTAHS Macarron MAI MAIT marr MatrixQCvis metabCombiner MetaboAnnotation MetaboAnnotatoR MetaboCoreUtils MetaboDynamics metabolomicsWorkbenchR metabom8 metabomxtr metaMS MetaPhOR metapone MetaProViz MetCirc MetMashR MetNet mixOmics MsBackendMassbank MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendRawFileReader MsBackendSql MsCoreUtils MsDataHub MsExperiment MsFeatures MSPrep msPurity msqrob2 MsQuality MWASTools mzR ncGTW netboost NormalyzerDE notame notameStats notameViz pairkat pathview pathwayPCA peakPantheR PepsNMR phenomis pmp ptairMS QFeatures qmtools RankProd rawDiag rawrr Rdisop RFLOMICS rgoslin RMassBank roastgsa ropls rWikiPathways SBGNview SDAMS seahtrue sfi SIMAT sparsenetgls Spectra SpectraQL SpectriPy squallms statTarget structToolbox timeOmics vsclust xcms yamss

Proteomics (193)

Aerith artMS ASEB AssessORF autonomics AWAggregator bandle bioassayR biobroom biosigner BRAIN BulkSignalR CalibraCurve calm Cardinal CausalR CellNOptR censcyt ChemmineOB ChemmineR Chromatograms cleaver clippda CNORdt CNORfeeder CNORode ComPrAn CONSTANd Coralysis cosmosR customProDB cydar CytoGLMM cytoKernel cytoMEM DAPAR deltaGseg DEqMS diffcyt diffuStats dmGsea DNEA DominoEffect Doscheda drawProteins drugTargetInteractions edgeR EGSEA eiR EWCE fCI fenr fmcsR funOmics GenProSeq GeomxTools glycoTraitR hdxmsqc HPAanalyze hpar HPiP idpr IMMAN immunogenViewer iModMix infinityFlow isobar IsoBayes KinSwingR koinar leapR limma limpa LimROTS MAPFX MassSpecWavelet MatrixQCvis MBQN MICSQTL mitch mixOmics MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendRawFileReader MsBackendSql MsCoreUtils MsDataHub MsExperiment msImpute msmsEDA msmsTests MSnbase MSnID mspms msqrob2 MsQuality MSstats MSstatsBig MSstatsBioNet MSstatsConvert MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsQC MSstatsQCgui MSstatsResponse MSstatsShiny MSstatsTMT mzID mzR NanoStringNCTools NormalyzerDE NPARC omicRexposome omicsGMF PAA Path2PPI pathview pathwayPCA PECA PepSetTest pepXMLTab pgca phenomis phosphonormalizer PhosR Pirat plaid plgem PLPE PolySTest PrInCE proBAMr proBatch PROcess procoil proDA pRoloc pRolocGUI PRONE Prostar ProteoDisco ProteoMM protGear ProtGenerics PSMatch PTMods Pviz qcmetrics QFeatures qPLEXanalyzer rain RankProd rawDiag rawrr RCASPAR Rcpi ReactomeGSA RFLOMICS roastgsa RolDE ropls ROTS rpx rScudo Rtpca SBGNview scp SDAMS SingleCellSignalR SMAD SmartPhos sparsenetgls SpatialOmicsOverlay specL Spectra SpectraQL SpectriPy squallms statTarget SubCellBarCode SWATH2stats TargetDecoy tidyexposomics timeOmics topdownr toppgene TPP TPP2D vsclust wpm XINA

Lipidomics (14)

biosigner CalibraCurve Cardinal DNEA lipidr LipidTrend LOBSTAHS MWASTools pathwayPCA RankProd rgoslin ropls squallms statTarget

Epigenetics (106)

Phylogenetics (16)

CIMICE cogeqc DECIPHER doubletrouble DspikeIn fastreeR ggtree ggtreeDendro ggtreeExtra ggtreeSpace orthogene rhinotypeR sitePath syntenet tanggle treeio

Pharmacogenomics (19)

ChemmineOB ChemmineR CoreGx DepInfeR drugTargetInteractions eiR faers fmcsR gCrisprTools gwasurvivr mslp octad PDATK PharmacoGx pogos RadioGx rcellminer ToxicoGx Xeva

Pharmacogenetics (16)

ChemmineOB ChemmineR DepInfeR drugTargetInteractions eiR fmcsR gCrisprTools mslp octad PDATK PharmacoGx RadioGx rcellminer toppgene ToxicoGx Xeva

Cheminformatics (19)

AlpsNMR ASICS BridgeDbR ChemmineOB ChemmineR CONSTANd customCMPdb drugTargetInteractions eiR fmcsR fobitools limma metabom8 MWASTools rcellminer Rcpi rmelting roastgsa seahtrue

StructuralGenomics (1)

QRscore

StructuralPrediction (11)

AlphaMissenseR BUMHMM circRNAprofiler DNAcycP2 DNAshapeR dStruct DuplexDiscovereR HiSpaR HPiP idpr ncRNAtools

Biophysics

MathematicalBiology (10)

AlphaBeta ClustIRR GenomAutomorphism IgGeneUsage ISoLDE missRows MouseFM queeems scoup sRACIPE

ComparativeGenomics (13)

AssessORF cbaf CCAFE cogeqc DECIPHER doubletrouble GenomAutomorphism MungeSumstats OmaDB orthogene scoup SynExtend syntenet

FunctionalGenomics (105)

airpart AlphaBeta AlphaMissenseR annotatr atena BasicSTARRseq BindingSiteFinder cageminer CAGEr CexoR chipenrich chromPlot COCOA cogeqc Cogito crisprBase crisprBowtie crisprBwa crisprDesign crisprScore crisprShiny crisprVerse crisprViz crumblr customProDB decoupleR DepInfeR DEWSeq DiffBind dmrseq doubletrouble dreamlet edgeR EGAD eisaR EpiCompare epidecodeR epiRomics EWCE fCCAC FGNet gCrisprTools gDNAx GenomAutomorphism GenomicDistributions GenomicOZone goatea GSVA heatmaps HiCPotts hpar HybridExpress idr2d ISAnalytics IsoformSwitchAnalyzeR limma lncRna loci2path LOLA maftools mariner memes metaseqR2 miloR MIRA MIRit ModCon MOMA MotifPeeker MouseFM mpra multistateQTL ncRNAtools NetActivity normr nullranges OmaDB OMICsPCA ORFik pathwayPCA pfamAnalyzeR planttfhunter plotgardener preciseTAD proActiv QTLExperiment rfaRm rigvf RITAN RIVER roastgsa scQTLtools screenCounter sevenC sincell sitadela spatzie splicelogic SurfR syntenet TENET tximeta VarCon variancePartition zenith

ComputationalChemistry

Agroinformatics

Transcriptomics (296)

ADImpute adverSCarial aggregateBioVar ALDEx2 AlphaMissenseR atena AUCell autonomics awst bacon bambu BASiCS BASiCStan batchelor BatchSVG Battlefield BayesSpace biosigner blacksheepr blase bluster broadSeq BulkSignalR BUMHMM CAGEfightR calm cardelino CARDspa carnation CARNIVAL CatsCradle CausalR cbaf ccfindR ccImpute cellity CellMentor CellMixS CEMiTool ceRNAnetsim chevreulPlot chevreulProcess chevreulShiny ClusterGVis clustSIGNAL concordexR condiments consensusOV consICA CONSTANd Coralysis cosmosR COTAN crumblr CTdata CTexploreR cTRAP CuratedAtlasQueryR dearseq DeconvoBuddies deconvR DeeDeeExperiment DELocal DenoIST DepecheR DEsingle DESpace diffuStats Dino dittoSeq dominoSignal dreamlet DropletUtils Dune DuplexDiscovereR edgeR eisaR epidecodeR escheR FLAMES funOmics gDNAx GeneStructureTools GeneTonic GenomicOZone GenomicSuperSignature GEOexplorer GeomxTools getDEE2 geva ggsc ggspavis globalSeq goatea GRaNIE granulator GraphExperiment GWENA hoodscanR HVP HybridExpress icetea ILoReg iModMix iNETgrate infercnv InterCellar iSEE iSEEfier iSEEu ISLET IsoformSwitchAnalyzeR jazzPanda KBoost kissDE KnowSeq leapR lemur limma M3Drop made4 markeR maser MAST mastR MatrixQCvis mbkmeans mdp megadepth MetaNeighbor metaseqR2 mitch MOGAMUN MoleculeExperiment MOMA mosdef NanoStringNCTools netboost netSmooth NewWave nnSVG omicplotR omicRexposome omicsGMF omicsPrint OmnipathR ompBAM orthogene OSTA.data OUTRIDER pathMED pathwayPCA peco pengls phantasus phantasusLite phenomis PICB Pigengene pipeComp PIPETS plyxp postNet ppcseq pram proActiv psichomics quantiseqr RankMap RCAS RcisTarget ReactomeGSA RegEnrich RegionalST retrofit RFGeneRank RFLOMICS rifi rifiComparative RIVER RNAdecay RNAshapeQC roastgsa ropls rScudo sarks satuRn SC3 scAnnotatR SCANVIS scater scBFA scBubbletree scCB2 scDiagnostics scds scECODA scFeatures scHOT scider scLANE scmap scMerge scMultiSim scone scran scrapper scReClassify scry scTypeEval scuttle SeqGate SEraster SETA shinyDSP singIST SingleCellAlleleExperiment SingleCellSignalR SingleR SiPSiC sitadela slalom slingshot smartid smoothclust smoppix sosta SpaceMarkers SpaceTrooper spacexr Spaniel SpaNorm spARI SpatialArtifacts SpatialCPie spatialDE SpatialDecon SpatialExperiment SpatialExperimentIO spatialFDA SpatialFeatureExperiment SpatialOmicsOverlay spatialSimGP SPICEY splatter splicelogic SpliceWiz SplicingFactory SplineDV SpNeigh SPONGE spoon SpotClean SpotSweeper ssPATHS STADyUM standR StatescopeR stJoincount stPipe SVMDO SVP switchde TENET tenXplore terapadog TFEA.ChIP TFutils tidybulk tidyexposomics tidyomics tidySpatialExperiment tidySummarizedExperiment tLOH tomoda tomoseqr topconfects topGO tpSVG tradeSeq TREG tricycle txcutr tximeta tximport UCell variancePartition veloviz visiumStitched VISTA Voyager weitrix wppi xCell2 zenith zinbwave

Epitranscriptomics (4)

epidecodeR EpiTxDb magpie raer

Immunology (423)

igblastr

Immunogenetics (1)

igblastr

ImmunoOncology (423)

AIMS ALDEx2 AlphaMissenseR amplican Anaquin anota2seq apComplex apeglm artMS ASpli atacInferCnv ATACseqQC attract bacon BADER ballgown bambu bandle banocc Basic4Cseq BASiCS BASiCStan BatchQC BayesSpace bayNorm bcSeq BEAT betaHMM BiFET bioassayR biomformat biotmle bluster BPRMeth BRAIN BUMHMM bumphunter calm CAMERA Cardinal casper CATALYST CausalR cbpManager ccfindR ccrepe celda cellity CellNOptR CellTrails CEMiTool censcyt CeTF CFAssay CHETAH chipenrich chromVAR cicero Clomial ClustIRR CNORdt CNORode COCOA CODEX CoGAPS compcodeR CONFESS coRdon coseq cosmiq countsimQC covEB CoverageView cqn CRISPRseek CrispRVariants cTRAP ctsGE customProDB cydar CytoDx CytoGLMM cytoKernel cytolib cytomapper CytoML CytoPipeline CytoPipelineGUI cytoviewer dada2 DaMiRseq dandelionR dcGSA dearseq debrowser decemedip DECIPHER decontam DeepTarget DEFormats DegNorm DEGreport DEGseq DepecheR DEqMS derfinder derfinderHelper derfinderPlot DEScan2 DESeq2 DEsingle DEsubs DEXSeq diffcoexp diffcyt DirichletMultinomial discordant dmrseq doppelgangR dreamlet DRIMSeq DropletUtils dupRadar easier easyRNASeq EBSeq EDASeq edgeR EGSEA EnhancedVolcano ENmix EnrichmentBrowser EpiDISH erccdashboard ERSSA esATAC EventPointer ExCluster flowAI flowBeads flowBin flowCHIC flowClean flowClust flowCore flowCyBar flowGate flowGraph flowMatch flowMeans flowMerge flowPeaks flowPlots flowSpecs flowStats flowTime flowTrans flowViz flowVS flowWorkspace gaga GAprediction GateFinder gCrisprTools GDCRNATools GeneStructureTools GenomicAlignments ggcyto GmicR GOexpress goseq goSTAG GOTHiC GRmetrics GSEABenchmarkeR GUIDEseq HDF5Array HTSFilter iASeq iasva Ibex icetea iCNV ideal igblastr IgGeneUsage IHW IMAS imcRtools immApex immLynx immunoClust immunotation INDEED InTAD IntEREst IPO iSEE iSEEfier iSEEu isobar IsoCorrectoR IsoCorrectoRGUI IsoformSwitchAnalyzeR ISoLDE isomiRs IVAS KnowSeq limma LimROTS Linnorm LOBSTAHS LoomExperiment M3C MACSr MAGAR MAIT MassArray MassSpecWavelet MCbiclust mCSEA Melissa metabomxtr MetaCyto metagenomeSeq metaMS MetaNeighbor metaSeq metaseqR2 methimpute methInheritSim MethPed methylInheritance MetNet mfa MGFR microbiomeExplorer minfi MIRA MiRaGE mixOmics MLSeq monocle MPAC MPRAnalyze msgbsR msmsEDA msmsTests MSnbase MSnID msqrob2 MSstats MSstatsBioNet MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsShiny MSstatsTMT mumosa muscat mzID mzR ncdfFlow netprioR NOISeq omicplotR omicRexposome OMICsPCA omicsPrint openCyto OPWeight ORFik Oscope OSTA.data OUTRIDER PAIRADISE pairedGSEA PANR PathoStat pcaExplorer pepXMLTab pgca phantasus phenopath philr phyloseq Pigengene plgem plotGrouper pogos POWSC prebs primirTSS proBAMr PROcess pRoloc PROPER ProteoMM protGear psichomics PureCN qcmetrics qPLEXanalyzer quantiseqr QuasR qusage Rcwl RcwlPipelines Rdisop recount recoup regionReport regsplice ReportingTools ReUseData rgsepd RiboDiPA RMassBank RNAdecay RNASeqPower RnaSeqSampleSize RnBeads roastgsa rols ropls ROTS rpx Rsubread RTCA RTCGA RUVSeq RVS sampleClassifier SC3 SCAN.UPC scater scDataviz scDD scde scFeatureFilter schex scmap scMET scmeth SCnorm scone Sconify scPipe scran scRepertoire scruff scuttle SDAMS SeqGSEA SGSeq SIAMCAT SigFuge sights signifinder SIMAT SIMD SIMLR simPIC sincell SingleCellAlleleExperiment SingleCellExperiment singleCellTK SiPSiC slalom SMITE SpaceTrooper sparsenetgls SpatialDecon SpatialExperiment SPIAT spillR splatter SplicingGraphs SPLINTER srnadiff sSeq ssviz staRgate statTarget stPipe strandCheckR subSeq sva SWATH2stats switchde synlet systemPipeR TargetSearch TCC tenXplore TFEA.ChIP timeOmics topdownr TPP transcriptogramer transcriptR treekoR Trendy tricycle tripr TRONCO tweeDEseq tximeta tximport Uniquorn uSORT variancePartition VaSP VDJdive vidger vmrseq wavClusteR wiggleplotr xCell2 xcms zenith zFPKM zinbwave

ImmunoPrevention

BiologicalQuestion (1015)

Coverage (159)

ACE animalcules ASpli ATACseqQC atena BadRegionFinder bambu bamsignals Basic4Cseq BasicSTARRseq baySeq BBCAnalyzer beer betaHMM BindingSiteFinder borealis BPRMeth breakpointR broadSeq BubbleTree BUMHMM CAGEfightR CeTF CexoR chevreulPlot chevreulProcess chevreulShiny ChIPanalyser ChIPexoQual chipseq ClonalSim CNAnorm CNVPanelizer CNVrd2 compEpiTools consensusSeekeR CopyNumberPlots csaw DAMEfinder DegNorm DeMixT derfinder DEScan2 diffcoexp diffHic dinoR DMCFB DMCHMM dmGsea DMRcaller DMRcate DropletUtils easylift edgeR ELViS EnrichedHeatmap ensembldb epiSeeker epistack esATAC extraChIPs fCCAC FRASER gDNAx GenomicAlignments GenomicDistributions GenomicFiles GenomicOZone GenomicPlot GenomicRanges GenomicScores gmoviz GreyListChIP HDF5Array HelloRanges HilbertCurve igvShiny IntEREst karyoploteR linkSet loci2path Macarron MBttest MDTS MEDIPS megadepth Melissa metagene2 methimpute methrix methylPipe miaSim MICSQTL MIRA NBAMSeq NewWave nucleR openPrimeR ORFik periodicDNA phenomis PhIPData PICB PIPETS plyranges profileplyr PureCN qsvaR QuasR raer ramwas RCAS recount recount3 recoup regionReport RepViz rGREAT RiboDiPA RiboProfiling ribosomeProfilingQC RJMCMCNucleosomes RNAshapeQC rprimer Rsamtools Scale4C scater scGPS scMET scone SCOPE seqCAT sevenC SICtools signatureSearch SMITE snapcount soGGi Spaniel SpliceWiz srnadiff strandCheckR SummarizedExperiment survtype svaRetro systemPipeR TFHAZ tidyCoverage topdownr transcriptR traseR TrIdent TVTB Ularcirc UMI4Cats uncoverappLib velociraptor VplotR wiggleplotr

DemethylateRegionDetection

DenovoAssembler

DifferentialDNA3DStructure

DifferentialExpression (397)

ABSSeq acde ADAPT affylmGUI aggregateBioVar AgiMicroRna airpart ALDEx2 AMARETTO AMOUNTAIN Anaquin ANCOMBC anota anota2seq APAlyzer apeglm artMS ASpli assorthead asuri atena autonomics BADER ballgown bambu BANDITS BASiCS BASiCStan BatchQC baySeq benchdamic biobroom BioNet biotmle blacksheepr blima BLMA broadSeq CAEN calm carnation casper CATALYST CausalR CellTrails Cepo CeTF circRNAprofiler clippda clusterSeq CNVRanger CoGAPS coGPS compcodeR consensusOV CONSTANd copa Coralysis Cormotif COTAN cqn crumblr csdR CTexploreR cTRAP ctsGE cummeRbund CuratedAtlasQueryR cytoKernel daMA damidBind DART dcanr ddCt dearseq debrowser DeconRNASeq decoupleR DeeDeeExperiment DeepTarget DEFormats DegNorm DEGraph DEGreport DEGseq DELocal DepecheR DEqMS derfinder derfinderHelper derfinderPlot DESeq2 DEsingle DESpace DEsubs DEWSeq DExMA DEXSeq DFP diffcoexp DifferentialRegulation diffGeneAnalysis distinct DMRcate DNEA doseR DOTSeq dreamlet DRIMSeq drugfindR DspikeIn DSS DTA EBarrays EBSEA EBSeq EDASeq edge edgeR EGSEA EMDomics EnhancedVolcano EnrichmentBrowser epidecodeR epigenomix epiregulon.extra erccdashboard ERSSA EWCE ExploreModelMatrix fabia factDesign fdrame fenr fgsea findIPs fishpond flagme gaga gage gatom gCrisprTools GDCRNATools gDNAx gemma.R genefu GeneSelectMMD geNetClassifier GeneTonic GenomicOZone GeoDiff GEOexplorer GeoTcgaData gep2pep geva gg4way GGPA GIGSEA Glimma GlobalAncova globalSeq globaltest goatea GOexpress goseq goSTAG GPA granulator GSALightning GSAR GSEABenchmarkeR gsean GSRI HDTD HEM hermes HIPPO HTqPCR HTSFilter hummingbird HybridExpress icetea iCheck ideal iGC IgGeneUsage ILoReg IMAS INDEED IntEREst iSEEde iSEEpathways ISLET IsoformSwitchAnalyzeR isomiRs IVAS IWTomics jazzPanda KnowSeq lefser lemur les limma limmaGUI limpa LimROTS Linnorm LipidTrend lmdme LPE LRcell LRDE M3Drop MAST mastR MBttest MEB MEDIPS messina metagenomeSeq MetaPhOR metaSeq metaseqR2 MethylMix microbiomeExplorer MIRit miRNApath mirTarRnaSeq mitch MODA MOGAMUN monocle Moonlight2R MoonlightR mosdef MPRAnalyze msqrob2 MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsShiny Mulcom MultiRNAflow multiWGCNA multtest muscat NanoStringDiff NanoTube NBAMSeq nempi netresponse NOISeq NoRCE NormalyzerDE OCplus oligo omicplotR omicRexposome omicsViewer oposSOM OrderedList orthos OutSplice PAIRADISE pairedGSEA PathNet pathview PECA PepSetTest phantasus phenoTest piano pickgene plgem PLPE PolySTest POWSC ppcseq proDA PRONE PROPER ProteoMM psichomics puma QRscore qsvaR QUBIC randRotation RankProd RBM recount recount3 RegEnrich regionReport regsplice RFLOMICS rgsepd RiboDiPA rifi rifiComparative RNAdecay RNAsense RNAseqCovarImpute RnaSeqSampleSize Rnits roastgsa ROC RolDE ROSeq ROTS rScudo RTCGAToolbox RUVSeq Rvisdiff safe sarks saseR satuRn SBGNview SC3 SCBN sccomp scDD scDDboost scde scDotPlot scLANE scMET scPCA scQTLtools scrapper SDAMS segmentSeq SeqGate SeqGSEA shinyDSP siggenes signatureSearch SIMD similaRpeak singleCellTK SiPSiC slingshot SmartPhos SMITE snm spacexr SpeCond SPICEY SpliceWiz SplineDV splineTimeR SpNeigh srnadiff ssize standR statTarget subSeq SurfR survcomp SVMDO switchde systemPipeTools tadar TBSignatureProfiler TCC TCGAbiolinks TCseq TEKRABber TENET tidybulk tidyexposomics tidyomics tidySingleCellExperiment tidySummarizedExperiment timecourse TOAST topconfects tradeSeq transcriptogramer transite tRanslatome treekoR TTMap tweeDEseq twilight unifiedWMWqPCR variancePartition VaSP vidger VISTA vsclust waddR webbioc xCell2 XDE zenith

DifferentialPeakCalling (15)

ChromSCape crupR csaw CSSQ derfinder DiffBind fourSynergy GreyListChIP IWTomics metapod MMDiff2 Motif2Site normr regionReport SPICEY

DNA3DStructure (12)

DNAshapeR FitHiC HicAggR HiCDCPlus HiCDOC HiCExperiment HiContacts HiCool hicVennDiagram idr2d sevenC spatzie

DriverMutation (2)

maftools MutSeqR

GeneFusionDetection (2)

DNAfusion Rsubread

GeneRegulation (116)

AffiXcan airpart AMARETTO anota2seq APAlyzer ATACseqQC ATACseqTFEA BasicSTARRseq BCRANK BiFET BindingSiteFinder BioNERO blima bnem BPRMeth BUMHMM CAGEfightR chromVAR cicero CNEr COCOA Cogito CRISPRseek damidBind decoupleR DegCre DEWSeq DiffBind diggit DOTSeq dreamlet eisaR ELMER enhancerHomologSearch epidecodeR epiregulon epiregulon.extra epiRomics epiSeeker FindIT2 GDCRNATools geneplast GenomicOZone GIGSEA GRaNIE GRENITS GSReg GSRI GUIDEseq idr2d IMAS INSPEcT ISoLDE IVAS KBoost LOLA MatrixRider Melissa memes methylGSA MethylMix MIRA MIRit miRSM Moonlight2R MoonlightR mpra NADfinder netZooR nullranges omicRexposome OmnipathR pandaR PIPETS postNet pqsfinder primirTSS proActiv profileScoreDist progeny projectR qpgraph RcisTarget regutools RiboDiPA ribosomeProfilingQC rifi rifiComparative rigvf RIVER RNAdecay Rsubread RTN RTNduals RTNsurvival rTRM rTRMui sarks scGraphVerse scMET SELEX spatzie SPICEY SPONGE sRACIPE TCGAbiolinks TENET terapadog TFBSTools TFEA.ChIP tigre tRanslatome triplex universalmotif viper xcore

GeneSetEnrichment (169)

ADAM ADAMgui AMARETTO artMS attract AUCell autonomics BgeeDB BioQC BLMA broadSeq bugsigdbr CAFE canceR carnation Category CBNplot CelliD chipenrich ChromSCape clusterProfiler CoGAPS cogena coRdon cpvSNP CSOA CTDquerier cTRAP ctsGE Damsel dcGSA dearseq DeepTarget dmGsea DOSE dreamlet drugfindR easier EasyCellType edgeR EGSEA EnrichDO EnrichmentBrowser enrichplot escape EWCE famat fedup fenr FGNet fgsea fobitools gage gCrisprTools GDCRNATools GeDi GeneTonic gep2pep GIGSEA GOaGO goatea GOexpress GOpro goProfiles goseq goSorensen goSTAG GOstats GRaNIE GSABenchmark GSALightning GSEABase GSEABenchmarkeR GSEAmining gsean GSReg GSRI GSVA GWENA hypeR ideal INTACT iSEEpathways ISoLDE KnowSeq leapR limma loci2path LOLA LRcell markeR MAST metaseqR2 methylGSA mgsa miRSM missMethyl mitch Moonlight2R MoonlightR mosdef multiGSEA MultiRNAflow NoRCE npGSEA nullranges octad omicsViewer oposSOM oppar pairedGSEA PanomiR PAST pathlinkR pathview pathwayPCA piano plaid PPInfer qusage RCAS RcisTarget ReactomeGSA ReactomePA RegEnrich ReportingTools rGREAT RGSEA rgsepd RITAN roastgsa RTN RTNsurvival safe SBGNview scGraphVerse scLANE SeqGSEA Seqtometry SGCP SigCheck simplifyEnrichment sincell singscore SiPSiC SmartPhos sparrow splineTimeR sSNAPPY SurfR SVMDO SVP systemPipeR TaxSEA terapadog TFEA.ChIP TissueEnrich TMSig topGO toppgene transcriptogramer transite ttgsea UCell variancePartition ViSEAGO vissE xCell2 zenith

GeneSignaling (13)

ASURAT cosmosR EGSEA escape hipathia MetaboSignal nempi OmnipathR pathwayPCA RankProd signifinder sSNAPPY wppi

GenomeAssembly (13)

bambu BSgenomeForge circRNAprofiler cogeqc easylift GenomicDistributions mobileRNA NoRCE plotgardener Seqinfo SMTrackR txdbmaker UCSC.utils

GermlineMutation (1)

plasmut

HistoneModification (8)

chipenrich crupR DiffBind epidecodeR epiRomics nullranges segmenter TENET

IndelDetection (2)

fRagmentomics Rsubread

LinkageDisequilibrium (5)

ASAFE CNVrd2 hierGWAS hierinf Qtlizer

MetagenomeAssembly

MicrosatelliteDetection

MotifDiscovery (14)

BCRANK magrene memes MotifPeeker omicsViewer periodicDNA PMScanR pqsfinder RCAS sarks SELEX TFBSTools toppgene universalmotif

NucleosomePositioning (9)

ATACseqQC dinoR methylscaper nucleR nuCpos NuPoP RJMCMCNucleosomes SMTrackR VplotR

QuantitativeTrailLocus

Scaffolding

SplicedAlignment (6)

DuplexDiscovereR gDNAx Guitar RgnTX Rhisat2 surfaltr

StructuralVariation (3)

FilterFFPE GenomicOZone infercnv

TranscriptomeVariant (6)

airpart IsoformSwitchAnalyzeR pfamAnalyzeR RIVER SplicingFactory transmogR

VariantDetection (13)

appreci8R ClonalSim CrispRVariants fRagmentomics infercnv lineagespot panelcn.mops PureCN Rsubread RVS scQTLtools SICtools svaRetro

WorkflowStep (1306)

Alignment (107)

amplican ASpli assorthead BadRegionFinder bambu bamsignals Basic4Cseq BBCAnalyzer bcSeq Biostrings BSgenomeForge chimeraviz ChIPanalyser ChIPexoQual cigarillo CircSeqAlignTk crisprBowtie crisprBwa DECIPHER DegNorm diffHic DiffLogo DominoEffect enhancerHomologSearch esATAC FilterFFPE fRagmentomics fraq gDNAx GenomicAlignments ggmsa ggseqalign ggtree gmapR GreyListChIP Guitar IMMAN IntEREst KnowSeq LymphoSeq metabom8 metagene2 MethTargetedNGS mitoClone2 mobileRNA MotifPeeker motifStack msa MSA2dist muscle ncGTW normr nucleoSim odseq ompBAM ORFik OUTRIDER periodicDNA ptairMS pwalign QSutils QuasR queeems R4RNA raer rBLAST Rbowtie Rbowtie2 Rbwa RcwlPipelines recoup RFGeneRank Rhisat2 RiboDiPA RiboProfiling rprimer Rsamtools Rsubread sangeranalyseR scanMiR SCOPE scoup screenCounter scruff segmentSeq seqcombo SICtools SimFFPE singleCellTK sitePath SpliceImpactR strandCheckR Structstrings surfaltr systemPipeR tanggle TFBSTools transmogR traseR treeio TVTB txcutr UMI4Cats VplotR

MultipleSequenceAlignment (19)

bcSeq fRagmentomics GenomAutomorphism ggmsa ggseqalign ggtree LymphoSeq msa muscle odseq R4RNA rfaRm rhinotypeR rprimer Rsubread sitePath surfaltr tanggle treeio

Annotation (150)

Aerith AlphaMissenseR altcdfenvs annaffy annmap annoLinker annotate AnnotationDbi AnnotationFilter AnnotationForge annotationTools annotatr APAlyzer artMS biobtreeR BiocIO biomaRt brendaDb BridgeDbR BSgenome BSgenomeForge CAGEfightR Category categoryCompare cellbaseR ChIPpeakAnno ChIPseeker chromPlot ChromSCape circRNAprofiler clusterProfiler clustifyr CompoundDb Coralysis csaw cytofQC DelayedArray DOSE DOtools ecolitk EnrichDO enrichplot epiSeeker escape FGNet FindIT2 fobitools garfield gemma.R GeneTonic genomation GenomeInfoDb genomes GenomicFeatures GenomicOZone GenomicPlot GenomicRanges GenomicScores ggmsa ggtree ggtreeExtra ggtreeSpace ginmappeR GOexpress GOfan GOpro goProfiles GOSemSim goseq goSorensen GOstats HDF5Array HelloRanges hypeR Ibex immApex immLynx immReferent immunotation intansv IsoformSwitchAnalyzeR KEGGREST matchBox MeSHDbi meshes meshr miRNApath mitoClone2 mygene myvariant nullranges occugene OGRE OmaDB OmicCircos OmnipathR Organism.dplyr OrganismDbi packFinder PCAN pdInfoBuilder pfamAnalyzeR plyxp podkat postNet quantiseqr raer RankMap ReactomePA rfPred rigvf rols rrvgo rsemmed rtracklayer SCANVIS scConform scDiagnostics scRepertoire SemDist Seqinfo sevenC simona SingleR Site2Target splicelogic SplicingGraphs StructuralVariantAnnotation SummarizedExperiment svaNUMT svaRetro SWATH2stats topGO treeio txcutr txdbmaker tximeta UCSC.utils Ularcirc uncoverappLib UniProt.ws VariantAnnotation VariantExperiment VariantFiltering VDJdive ViSEAGO vsclust wppi xmapbridge yarn

MultipleComparison (180)

abseqR ADAPT affylmGUI AMARETTO anglemania artMS ASSET asuri bacon bambu BANDITS baySeq benchdamic betaHMM biobroom bioCancer bumphunter calm canceR categoryCompare CGEN ChIPseeker ChromSCape clippda Clomial clusterProfiler clusterSeq cnvGSA CoGAPS compSPOT condiments consensusSeekeR CoSIA csaw cydar cytomapper dar DEqMS DiffBind DifferentialRegulation diffHic DiffLogo distinct dks DMRcate dmrseq DOSE DOTSeq DRIMSeq EBSeq edge edgeR EGSEA EpiCompare epiSeeker erccdashboard ERSSA fabia fdrame FindIT2 fishpond gaga gage gCrisprTools GeneOverlap geva GEWIST GGPA globalSeq GOexpress GOpro goProfiles goSorensen GOstats GPA hammers Harman HTqPCR iGC IHW IsoformSwitchAnalyzeR ISoLDE IWTomics LBE limma limmaGUI limpca LinkHD looking4clusters maaslin3 made4 matchBox MBttest mCSEA meshes MetaboDynamics metagene2 metagenomeSeq MetaNeighbor metapod metaseqR2 microbiomeExplorer MicrobiotaProcess microSTASIS miloR mixOmics monocle MotifPeeker MouseFM msa msqrob2 Mulcom MultiMed multtest nipalsMCIA NormalyzerDE normr notame notameStats notameViz OCplus omicade4 omicRexposome OMICsPCA onlineFDR openPrimeR OPWeight OrderedList OVESEG parody PathNet pathwayPCA phenoTest PhyloProfile phyloseq plotGrouper PROMISE psichomics qsmooth quantro QUBIC R4RNA raer rain ReactomePA reconsi regioneReloaded rexposome rhinotypeR roastgsa satuRn scDD Sconify scShapes segmentSeq semisup seqsetvis SIAMCAT siggenes sights SimFFPE similaRpeak snm SpeCond ssviz statTarget surfaltr sva swfdr TENET tidyexposomics timeOmics topconfects tradeSeq tripr TTMap TVTB twilight unifiedWMWqPCR ViSEAGO

Normalization (188)

ACME ADAPT affylmGUI AMARETTO ANCOMBC anota2seq artMS assorthead AUCell awst bambu BASiCS BASiCStan batchCorr batchelor BatchQC bayNorm benchdamic betterChromVAR blima bnbc BOBaFIT CAGEfightR CAGEr Cardinal CATALYST cellity CeTF ChAMP chevreulPlot chevreulProcess chevreulShiny ChromSCape CNAnorm CNVPanelizer CODEX CONSTANd conumee CPSM CrcBiomeScreen crumblr csaw CSSQ CuratedAtlasQueryR cytomapper DAPAR dar DCATS DegNorm DEqMS DESeq2 DEsubs DiffBind diffHic diffuStats Dino dominatR Doscheda dreamlet DspikeIn edgeR ELViS EnMCB ENmix epimutacions epiregulon.extra fishpond flowSpecs funtooNorm gCrisprTools gemma.R GeoDiff GeomxTools GladiaTOX Harman hermes HicAggR HiCcompare HiCDCPlus HiCDOC HTSFilter iNETgrate IntEREst KnowSeq limma limmaGUI Linnorm lipidr Maaslin2 maaslin3 MACSQuantifyR MANOR MBECS MBQN MEAT MEB metagenomeSeq metaseqR2 methylclock microbiomeExplorer minfi missMethyl msqrob2 MSstats MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsQC MSstatsShiny multiHiCcompare MultiRNAflow NanoStringDiff netSmooth nipalsMCIA normalize450K NormalyzerDE normr notame notameStats notameViz omicsGMF phantasus phenomis phosphonormalizer Pigengene PLSDAbatch POMA ppcseq proBatch proDA PRONE Prostar ProteoMM protGear qmtools qPLEXanalyzer qsea qsmooth qsvaR quantro ramwas randRotation rgoslin RiboDiPA RNAdecay Rnits roastgsa RUVcorr RUVnormalize SanityR scater SCBN scECODA scHiCcompare scMerge SCnorm scone SCOPE scQTLtools scran scrapper scry scuttle SETA sigFeature sights simpleSeg singleCellTK slalom SmartPhos Spaniel spiky spqn standR statTarget sva TEKRABber tidybulk tidyomics tidySingleCellExperiment tidySummarizedExperiment transformGamPoi TurboNorm UMI4Cats variancePartition Wrench yarn zenith

Pathways (205)

ADAM ADAMgui anansi annaffy annotate ASSIGN attract bioCancer BioCartaImage BioCor BLMA bnem carnation Category categoryCompare CBN2Path CBNplot CellNOptR CEMiTool ChromSCape CHRONOS clusterProfiler cogena coRdon cosmosR cpvSNP CTDquerier cTRAP DART DeeDeeExperiment DeepTarget DEsubs dmGsea DOSE easier edgeR EGSEA EmpiricalBrownsMethod EnrichmentBrowser enrichplot epiNEM escape esetVis famat fastLiquidAssociation fedup FELLA FGNet fgsea fobitools funOmics gage gatom GeDi GeneTonic GenomicSuperSignature gep2pep ggkegg GlobalAncova globaltest GOexpress goProfiles GOSemSim goseq goSorensen GOstats graphite GSEABenchmarkeR gsean GSReg GSVA GWENA hipathia hypeR iPath iSEEpathways islify KEGGgraph KEGGlincs keggorthology KEGGREST KnowSeq leapR LiquidAssociation MetaboDynamics MetaboSignal MetaPhOR metapone MetaProViz methylGSA MethylMix mgsa mirIntegrator MIRit miRNApath mitology MLP mnem Moonlight2R MoonlightR MOSClip multiGSEA MultiRNAflow NCIgraph ndexr nempi NetActivity NetPathMiner npGSEA occugene OmnipathR oppar padma pairedGSEA pairkat PanomiR PAST Path2PPI pathlinkR pathMED PathNet pathRender pathview pathwayPCA PCAN PhenoGeneRanker piano PPInfer qpgraph RCX ReactomePA rGREAT roastgsa rrvgo rsbml rsemmed safe SBGNview SBMLR scGraphVerse scToppR sparrow ssPATHS SurfR TCGAbiolinks tidysbml TMSig topGO toppgene transomics2cytoscape wppi

Reactome (22)

attract bioCancer CBNplot clusterProfiler famat fenr GeDi goSorensen graphite MetaboSignal mitch mitology MLP MOSClip multiGSEA pathlinkR ReactomeGSA ReactomePA RegionalST scGraphVerse slalom terapadog

BioCarta (5)

BioCartaImage loci2path multiGSEA padma UniProt.ws

NCINatureCurated

Preprocessing (272)

a4Preproc ABarray ADImpute affy affycomp affyILM affylmGUI affyPLM AffyRNADegradation AgiMicroRna AlpsNMR altcdfenvs AMARETTO Anaquin aroma.light ARRmNormalization atena autonomics AWAggregator ballgown barbieQ BatchQC beadarray BEclear benchdamic BERT bigmelon BioNERO biovizBase blima bnbc bnem BreastSubtypeR BUS CAGEfightR CAGEr CATALYST cbpManager CCAFE CellBarcode cellity CGHcall CGHnormaliter chevreulPlot chevreulProcess chevreulShiny ChromSCape clippda CluMSID codelink CompensAID CONSTANd conumee corral covEB CPSM cqn crlmm crumblr cytolib CytoPipeline CytoPipelineGUI DAPAR DEGseq demuxmix DenoIST DEqMS DEsingle diffHic DMRcate DNABarcodeCompatibility DNABarcodes Doscheda dreamlet DspikeIn dyebias easyRNASeq EDASeq ENmix EpiMix epimutacions epistack esATAC ExiMiR FilterFFPE flowCut flowGate flowWorkspace frenchFISH frma frmaTools funtooNorm gCrisprTools gcrma gDNAx gemma.R genArise GGPA GladiaTOX GOTHiC GPA GreyListChIP Harman HELP hermes HMMcopy HTqPCR HTSFilter iasva iBMQ iCheck imageTCGAutils IsoCorrectoR IsoCorrectoRGUI KnowSeq limma limmaGUI limpa lumi maCorrPlot MACSQuantifyR MAGAR makecdfenv MANOR marray matter MBCB MBQN MEAT MEDIPS megadepth metabom8 MetaCyto metaseqR2 methylclock methylumi Mfuzz MiChip minfi miQC miRcomp miRNAmeConverter mobileRNA mspms MSPrep msqrob2 MultiRNAflow multiscan MungeSumstats mutscan netprioR netSmooth nipalsMCIA nnNorm nnSVG nondetects normalize450K normr notame notameStats notameViz NTW oligo OLIN OLINgui omicsGMF openCyto orthogene PeacoQC peakCombiner PepsNMR pepStat piano Pirat POMA prebs primirTSS proActiv proBatch PRONE Prostar protGear ptairMS puma QDNAseq qmtools qpcrNorm qPLEXanalyzer qsea qsmooth quantro QuasR r3Cseq R4RNA ramwas randRotation RankMap Rbowtie2 rCGH RcwlPipelines recoup REDseq REMP ReUseData Rfastp rgoslin RnBeads roastgsa RPA Rsubread RTCGA RUVSeq sangeranalyseR SCAN.UPC scater scCB2 scDblFinder scds scECODA scFeatureFilter scifer scmap scmeth scMitoMut scone scp scPipe scQTLtools scruff scTypeEval scuttle seahtrue SEraster sesame shinyepico shinyMethyl SIAMCAT sights skewr SmartPhos snm Spaniel spiky spillR spoon SpotClean squallms srnadiff staRgate statTarget stepNorm stPipe sva SWATH2stats synlet SynMut TargetSearch TCGAutils tilingArray tpSVG transformGamPoi tRNAscanImport TurboNorm tximeta tximport UMI4Cats variancePartition VaSP vsn wateRmelon yarn zenith

QualityControl (243)

abseqR Aerith affylmGUI affyPLM AffyRNADegradation airpart alevinQC altcdfenvs AMARETTO arrayMvout arrayQuality arrayQualityMetrics artMS AssessORF assorthead ATACseqQC bandle basecallQC Basic4Cseq batchCorr BatchQC BatchSVG beadarray BERT bigmelon BioQC CaMutQC CellBarcode cellity chevreulPlot chevreulProcess chevreulShiny ChIPexoQual ChIPQC chipseq ChromSCape CleanUpRNAseq clstutils CODEX cogeqc CompensAID CONFESS consensus conumee countsimQC CRISPRball crumblr cummeRbund CuratedAtlasQueryR CytoMDS CytoPipeline CytoPipelineGUI DAPAR DECIPHER DegNorm DExMA DiscoRhythm dks DMRcate doppelgangR Doscheda DOtools dreamlet DspikeIn dupRadar dyebias EDASeq edgeR ENmix EpiCompare erccdashboard ERSSA esATAC FastqCleaner ffpe FilterFFPE flowAI flowClean flowCut fraq GBScleanR gCrisprTools GENESIS ggspavis GladiaTOX GloScope GmicR Guitar GWASTools hdxmsqc HELP hermes HTqPCR iasva ibh iCheck ideal IONiseR isobar KnowSeq limma limmaGUI lipidr lncRna lumi MAGAR MANOR marr massiR MatrixQCvis MBECS mdp mdqc MDSvis MEDIPS MetaProViz metaseqR2 MethylAid methylumi minfi miQC miRcomp mobileRNA monocle MotifPeeker MSnbase MsQuality MSstats MSstatsBioNet MSstatsConvert MSstatsLiP MSstatsLOBD MSstatsPTM MSstatsQC MSstatsQCgui MSstatsShiny MWASTools NanoTube ngsReports notame notameStats notameViz nucleR OLIN OLINgui omicsGMF omicsPrint Omixer omXplore OSAT pcaExplorer PeacoQC phenomis piano pmp ppcseq proBatch proDA pRoloc pvac qcmetrics QDNAseq qPLEXanalyzer qsea QuasR R453Plus1Toolbox RadioGx ramwas RcwlPipelines recoup regionReport REMP Rfastp RiboDiPA RiboProfiling ribosomeProfilingQC RITAN rnaseqcomp RNAshapeQC RnBeads roastgsa RPA Rqc Rsamtools Rsubread sangeranalyseR Scale4C scater scBFA scds scifer scmeth scone SCOPE scPipe scrapper scruff scTGIF scuttle seahtrue segmentSeq sesame shinyepico shinyMethyl ShortRead SICtools sights singleCellTK skewr SmartPhos SNAGEE snm SpaceTrooper Spaniel SpatialArtifacts SPIAT spikeLI spiky SpotSweeper squallms standR statTarget stPipe strandCheckR synlet systemPipeR systemPipeShiny systemPipeTools TargetDecoy TEQC tidybulk tidyexposomics tidyomics tidySingleCellExperiment tidySummarizedExperiment tRanslatome traseR UMI4Cats unifiedWMWqPCR variancePartition wateRmelon yarn zenith

Visualization (609)

abseqR ACE Aerith AlpsNMR animalcules annmap annoLinker annotatr aroma.light arrayQuality AssessORF atSNP BANDITS barbieQ barcodetrackR Basic4Cseq BatchQC bettr bioassayR bioCancer BioCartaImage biocGraph BiocPkgDash BioMVCClass biomvRCNS biovizBase BloodGen3Module BOBaFIT BreastSubtypeR BrowserViz CAGEfightR CAGEr CalibraCurve cancerclass cardelino CARDspa carnation CATALYST CBNplot cbpManager CCPlotR CDI cellity cellscape cfDNAPro CGHcall CGHregions ChemmineOB ChemmineR chevreulPlot chevreulProcess chevreulShiny ChIPexoQual ChIPseeker ChromHeatMap chromPlot ChromSCape clevRvis cliProfiler ClonalSim clstutils clustComp ClusterGVis clusterProfiler CNEr CNVfilteR CNViz cogena comapr combi compEpiTools ComplexHeatmap ComPrAn condiments CONFESS copa CopyNumberPlots coRdon corral countsimQC CoverageView CPSM CrcBiomeScreen CRISPRball CrispRVariants ctc cummeRbund CytoMDS CytoPipeline CytoPipelineGUI dagLogo damidBind DECIPHER DEGreport deltaGseg densvis DepecheR derfinderPlot DESpace destiny DEXSeq DifferentialRegulation DiffLogo DiscoRhythm distinct dittoSeq dominatR DOSE DOtools drawProteins DspikeIn Dune EBImage ecolitk eiR ELViS EnrichDO EnrichedHeatmap EnrichmentBrowser enrichplot epiRomics epiSeeker epivizr epivizrChart epivizrData epivizrServer epivizrStandalone escheR esetVis EWCE fabia FGNet FinfoMDS fishpond flowcatchR flowCHIC flowClust flowCyBar flowFP flowGraph flowPloidy flowPlots FlowSOM flowSpecs flowTime flowViz fmcsR fobitools gCrisprTools GDCRNATools GeDi GeneBreak genefu GeneOverlap geneplotter GeneRegionScan GeneTonic genomation GenomicDistributions GenomicOZone GenomicPlot geomeTriD gg4way ggbio ggcyto ggmanh ggmsa ggsc ggseqalign ggtree ggtreeDendro ggtreeExtra ggtreeSpace gINTomics Glimma glycoTraitR gmoviz goatea GOexpress GOfan goSTAG goTools GRmetrics GSABenchmark GSCA GSEABenchmarkeR GSEAmining gtrellis gVenn Gviz GWENA hammers hapFabia heatmaps Heatplus HELP HicAggR hicVennDiagram HilbertCurve HilbertVis HilbertVisGUI HistoImagePlot HMMcopy HPAanalyze HTqPCR hyperdraw iCOBRA ideal IdeoViz idiogram igvR ILoReg ImageArray immunogenViewer iModMix interacCircos InteractiveComplexHeatmap InterCellar iSEE iSEEfier iSEEpathways iSEEtree iSEEu islify IsoBayes IsoformSwitchAnalyzeR ivygapSE karyoploteR KCsmart KEGGgraph keggorthology limpca lipidr LipidTrend lmdme lncRna looking4clusters maCorrPlot maftools mapscape mariner markeR maser MassArray mastR matchBox MatrixQCvis MBECS MDSvis MEDIPS metagenomeSeq MetaProViz MetCirc MethylAid methylscaper Mfuzz miaDash miaViz microbiomeDASim microbiomeExplorer MicrobiomeProfiler MicrobiotaProcess MICSQTL mimager missRows mitology mobileRNA MOFA2 monaLisa monocle mosdef motifbreakR motifStack MultiRNAflow multistateQTL muscat MutSeqR MVCClass NanoMethViz ncRNAtools Nebulosa NOISeq NormalyzerDE notame notameStats notameViz nullranges NuPoP OGRE OLIN OLINgui OmicCircos omicplotR omicRexposome omicsGMF OMICsPCA omicsViewer Omixer oposSOM OSAT PANR PathoStat pathRender pathview pcaExplorer peco Pedixplorer PepsNMR phantasus PhyloProfile piano plotgardener PLSDAbatch PMScanR poem POMA proBAMr proBatch pRolocGUI PRONE psichomics Pviz qcmetrics qsea quantiseqr quantsmooth QUBIC R453Plus1Toolbox R4RNA ramwas RCASPAR rcellminer RCM RCSL RCy3 RCyjs RDRToolbox ReactomePA regionReport regutools ReportingTools RepViz retrofit rfaRm RFGeneRank rGenomeTracks RGraph2js Rgraphviz rhinotypeR riboSeqR ribosomeProfilingQC RNAmodR RNAmodR.AlkAnilineSeq RNAmodR.ML RNAmodR.RiboMethSeq rnaseqcomp RTCA RTCGA rtracklayer Rvisdiff rWikiPathways sangeranalyseR sangerseqR satuRn SBGNview SC3 Scale4C SCANVIS scater scatterHatch scBubbletree scDD scDotPlot scECODA scGraphVerse schex scLANE scLang scmap Sconify scPassport scPipe scQTLtools scRNAseqApp scruff scTreeViz seahtrue sechm seqcombo seqPattern seqsetvis SETA SGCP shiny.gosling SigFuge sights signeR signifinder SIM simplifyEnrichment sincell slalom slingshot SmartPhos SMTrackR snifter SomaticSignatures sosta Spaniel sparsenetgls spatialHeatmap SpatialOmicsOverlay SPIAT spillR SplicingGraphs SPLINTER splots squallms ssviz statTarget stPipe surfaltr SurfR survcomp synlet tanggle TargetDecoy TCseq TENET tidyexposomics tidyprint tilingArray timescape TMSig TnT tomoda tomoseqr topGO trackViewer tradeSeq transcriptogramer TreeAndLeaf treekoR tRNA tRNAdbImport tRNAscanImport TSAR TSCAN TVTB Ularcirc UMI4Cats uncoverappLib unifiedWMWqPCR VaSP veloviz VennDetail vidger ViSEAGO visiumStitched VISTA Voyager vsclust wiggleplotr xmapbridge YAPSA yarn

Network (165)

ADImpute AMARETTO AMOUNTAIN ANF annoLinker BayesKnockdown bioCancer BioCor BioNAR BioNERO BioNet BiRewire bnem BulkSignalR cageminer CARNIVAL CausalR CBNplot CCPlotR CellNOptR CEMiTool ceRNAnetsim CeTF cliqueMS CNORfuzzy cogeqc cosmosR COSNet csdR CTDquerier dcanr decoupleR DeepPINCS DEGraph DeMAND DEsubs diffuStats DNEA dominoSignal doubletrouble DriverNet drugfindR EGAD EGSEA ELMER EnrichmentBrowser enrichViewNet epiNEM epiregulon epiregulon.extra ExpoRiskR fedup FELLA fgga FGNet gatom GDCRNATools GENIE3 glmSparseNet GmicR GNET2 goatea GOSemSim GraphAlignment GraphAT GraphExperiment graphite GRENITS GSEABenchmarkeR gsean GWENA HPiP IMMAN iModMix iNETgrate Informeasure KBoost KEGGlincs KinSwingR levi Linnorm lionessR LiquidAssociation MAGAR martini MetaboSignal MethylMix MetID MetNet miaSim minet mirIntegrator MIRit miRLAB mnem MODA MOGAMUN MOMA Moonlight2R MoonlightR MSstatsBioNet ndexr nempi netboost NetPathMiner netprioR netresponse netSmooth netZooR omicsViewer OmnipathR pageRank pairkat pandaR Path2PPI pathifier pathlinkR PathNet PCAN PhenoGeneRanker Pigengene PIUMA postNet PPInfer QUBIC R3CPET RBGL RCX RCy3 RedeR ReducedExperiment RegEnrich regutools RGraph2js RITAN RLassoCox rrvgo rsbml rScudo RTN rTRM rTRMui rWikiPathways SANTA SBMLR scGraphVerse SGCP SingleCellSignalR SMITE spatialHeatmap SPEM STRINGdb syntenet TCGAbiolinks ternarynet tidysbml toppgene transcriptogramer transomics2cytoscape TreeAndLeaf TRONCO vissE vtpnet wppi XINA

GenomeBrowsers (2)

CAGEfightR igvR

WorkflowManagement (1)

systemPipeR

StatisticalMethod (874)

AMARETTO APL ASSET asuri AWFisher bacon ballgown BANDITS BEclear beer BioCor BiocSklearn BioQC BUScorrect BUSseq CATALYST CatsCradle CBN2Path CIMICE ClustAll ClusterJudge ClusterSignificance consICA covEB cpvSNP CTSV CytoDx CyTOFpower CytoGLMM dcGSA decompTumor2Sig deconvR decoupleR deltaCaptureC DeMAND DeMixT DESpace DExMA DifferentialRegulation discordant distinct divergence dStruct EBSeq EmpiricalBrownsMethod epimutacions fabia FeatSeekR fgga flowGraph garfield GENESIS GGPA glmSparseNet GPA granulator GSAR gscreend gsean Harman HDTD HIBAG HiCPotts HiLDA iasva iCARE INDEED infercnv IntramiRExploreR IsoBayes IsoformSwitchAnalyzeR IWTomics jazzPanda kmcut LACHESIS lefser Lheuristic limpca LipidTrend MAI mbQTL MCbiclust MDTS MeasurementError.cor MeLSI metaCCA MetaCyto methInheritSim methylclock methylInheritance MethylMix MetID midasHLA missRows mogsa MOSClip MPRAnalyze MSstatsResponse Mulcom MultiBaC MultiMed muscat MutSeqR netboost npGSEA nucleoSim omicRexposome onlineFDR OpenStats ORFhunteR Oscope padma pageRank PAIRADISE pandaR peco phenomis phosphonormalizer plotGrouper PLSDAbatch POMA PPInfer profileScoreDist QRscore quantiseqr QUBIC queeems randPack randRotation RankProd receptLoss regionalpcs RFGeneRank RGSEA RJMCMCNucleosomes ROCpAI RolDE rqt RUVnormalize safe SAIGEgds scde scoup selectKSigs SETA signeR SNPRelate SomaticSignatures spaSim spillR SpliceImpactR SPOTlight srnadiff STADyUM stageR STATegRa Summix survtype sva swfdr switchBox synergyfinder target TFARM tidyexposomics TMixClust tpSVG TrajectoryGeometry treeclimbR treekoR tweeDEseq Uniquorn VaSP waddR XAItest YAPSA zitools

Classification (189)

a4Classif a4Core adverSCarial AIMS AlpsNMR antiProfiles BadRegionFinder bandle BiocNeighbors bioDist biosigner BreastSubtypeR BUMHMM CAEN cancerclass Cardinal Cepo CHETAH ChromSCape ClassifyR clst clstutils ClusterSignificance ClustIRR CMA CNVPanelizer cola compSPOT CONFESS consensusOV consICA Coralysis CoreGx COSNet CrcBiomeScreen CRImage ctc CytoDx cytoMEM dada2 DaMiRseq decontam DeMixT demuxmix demuxSNP DepecheR DirichletMultinomial dominatR doubletrouble easier EGSEA epigenomix escape evaluomeR fastseg fgga flowcatchR gaga GARS geneClassifiers genefu geNetClassifier GenVisR geva GGPA ggtreeDendro glmSparseNet GPA gpls GrafGen graper GSgalgoR HiCPotts HybridExpress Ibex iCOBRA idr2d immApex immLynx iNETgrate islify iterativeBMA jvecfor katdetectr kebabs KnowSeq LedPred lefser LinkHD lncRna logicFS looking4clusters made4 maftools MAI maPredictDSC markeR massiR MEB messina metabinR metagenomeSeq MethPed microbiomeExplorer MiPP miRNAtap mixOmics MLInterfaces MLSeq MPRAnalyze nempi NetPathMiner nipalsMCIA normr NuPoP octad omicade4 ORFhunteR PAA partCNV pathMED pathwayPCA PDATK peco PharmacoGx phenoTest phyloseq Pigengene PIUMA planttfhunter PLSDAbatch PoDCall Polytect POMA preciseTAD procoil pRoloc PROPS quantiseqr queeems RadioGx rexposome RFGeneRank rfPred RGSEA Rmagpie ROCpAI ropls rScudo sampleClassifier SC3 scAnnotatR scClassify scConform scDiagnostics scds SCFA scmap scoup scReClassify scRepertoire SemDist semisup sevenC SGCP SIAMCAT SigCheck sigFeature simpleSeg singIST SingleR SpatialArtifacts spatzie squallms ssPATHS Statial SubCellBarCode supersigs survClust SVMDO switchBox timeOmics TrIdent TTMap twoddpcr vbmp wavFeatExt XAItest Xeva

Clustering (287)

adSplit airpart AMARETTO ANF artMS ASURAT bandle Banksy BayesSpace BicARE BiocNeighbors BioCor bioDist bluster BOBaFIT BPRMeth BUScorrect BUSseq CAGEr canceR Cardinal CATALYST ccfindR ccImpute CDI celda CelliD cellmig CellTrails censcyt CGEN ChemmineOB ChemmineR CHETAH ChromSCape cicero Clomial CluMSID ClustAll clustComp clusterExperiment ClusterFoldSimilarity ClusterGVis ClusterJudge clusterProfiler clusterSeq ClusterSignificance clusterStab ClustIRR clustSIGNAL CoGAPS cogena cola concordexR CONFESS ConsensusClusterPlus consensusOV Coralysis COTAN crumblr ctc ctsGE cummeRbund CuratedAtlasQueryR cyanoFilter cytoKernel cytoMEM ddPCRclust debrowser DECIPHER deltaGseg DepecheR DESeq2 destiny diffcyt diffHic DirichletMultinomial DNEA DOtools DrugVsDisease Dune DuplexDiscovereR EBarrays edgeR eiR ELViS evaluomeR fabia fastreeR fcScan FEAST FGNet flowCHIC flowClust flowCyBar flowDensity flowFP flowMatch flowMeans flowMerge flowPeaks FlowSOM fmcsR FuseSOM GARS GateFinder GeDi genefu geneRecommender geneRxCluster GenomicOZone GenomicSuperSignature GGPA ggtree ggtreeDendro GmicR GOexpress GOpro GOSemSim goSorensen goSTAG GPA GSEAmining GSgalgoR GWENA hapFabia HGC HiCDOC hierGWAS hierinf HIPPO hoodscanR hopach ILoReg imcRtools immLynx immunoClust iModMix iNETgrate iSEE iSEEfier iSEEu isomiRs jvecfor kebabs LEA limma Linnorm looking4clusters M3C Macarron made4 MAGAR MantelCorr MAPFX massiR mbkmeans MCbiclust Melissa meshes metabinR MetaboDynamics MetaCyto MetaDICT metagenomeSeq MetaProViz metaseqR2 Mfuzz microbiomeExplorer microSTASIS miRSM MLInterfaces MLSeq mobileRNA MOGAMUN mogsa MOMA monocle MPAC multiClust MultiRNAflow multiWGCNA netboost nethet NetPathMiner netresponse netSmooth nipalsMCIA omada omicade4 OMICsPCA PANR PDATK phantasus phenomis phenoTest phyloseq Pigengene pipeComp PIUMA poem Polytect POMA powerTCR ppcseq preciseTAD pRoloc protGear puma QUBIC RCSL RDRToolbox regioneReloaded rexposome Rigraphlib RIVER roastgsa rrvgo rScudo SANTA SC3 scBubbletree scCB2 scDD scDDboost scDiagnostics scDotPlot scECODA SCFA scGPS scLANE scMET scran scrapper selectKSigs semisup SGCP SIAMCAT SigFuge SIMLR simplifyEnrichment sincell singleCellTK SingleR slingshot SmartPhos smoothclust SomaticSignatures Spaniel spARI SpatialCPie spatialHeatmap SpeCond SpectralTAD SPIAT squallms STATegRa stJoincount stPipe survClust survtype SynExtend systemPipeShiny systemPipeTools TADCompare tanggle TCseq tidybulk tidyomics tidySingleCellExperiment tidySummarizedExperiment timeOmics TMixClust TMSig tomoda toppgene tradeSeq transcriptogramer treeio treekoR TRONCO TTMap VaSP ViSEAGO vsclust YAPSA yarn

DecisionTree (8)

CMA DEGraph GENIE3 ggtreeDendro mistyR Pigengene POMA TargetSearch

GraphAndNetwork (131)

airpart ANF apComplex BatchQC biocGraph BioMVCClass BioNAR BioNERO BioNet CausalR CBN2Path CEMiTool ceRNAnetsim CHRONOS CIMICE ClusterFoldSimilarity COSNet csdR DART dcanr DeepPINCS DEGraph DEsubs diffuStats EGAD EGSEA EnrichmentBrowser epiregulon.extra FELLA fgga fobitools GeneNetworkBuilder GENIE3 glmSparseNet GmicR goProfiles goSorensen GOstats GRaNIE graph GraphAlignment GraphAT graphite GRENITS GSEABase GSEABenchmarkeR gsean GWENA HGC hipathia hyperdraw hypergraph ibh IMMAN iNETgrate jvecfor KBoost KEGGgraph KEGGlincs keggorthology MAGAR magrene martini MetaboSignal minet mirIntegrator MOGAMUN MOSClip MVCClass NCIgraph netboost nethet NetPathMiner netresponse netSmooth netZooR OmnipathR paircompviz pairkat pandaR PANR PathoStat pathRender pathview Pedixplorer PhenoGeneRanker Pigengene PIUMA plotGrouper poem PPInfer qpgraph QuaternaryProd R3CPET RBGL RCy3 RCyjs RedeR RGraph2js Rgraphviz Rigraphlib RITAN rsbml rScudo RTN RTNduals RTNsurvival rTRM rTRMui rWikiPathways SBGNview SBMLR scGraphVerse SGCP sincell sparsenetgls spatialHeatmap SPIA SpiecEasi splineTimeR spqn syntenet ternarynet tidyexposomics tidysbml TMSig transcriptogramer TreeAndLeaf TRONCO VennDetail wppi

HiddenMarkovModel (16)

betaHMM BUMHMM DMCHMM epigraHMM frenchFISH GBScleanR HiCPotts hummingbird iCNV infercnv methimpute nullranges NuPoP partCNV planttfhunter UPDhmm

MultidimensionalScaling (5)

CytoMDS FinfoMDS MDSvis POMA systemPipeTools

NeuralNetwork (5)

COSNet DeepPINCS DNAcycP2 nempi SGCP

PatternLogic (3)

MouseFM PathoStat TrIdent

Regression (155)

AffiXcan affylmGUI airpart AMARETTO anansi anota2seq asuri autonomics AWAggregator bacon bambu barbieQ biobroom biotmle BPRMeth BUMHMM CalibraCurve calm Cardinal cellmig CeTF CFAssay chipenrich CONFESS consensus crumblr CTSV CytoDx CytoGLMM dearseq deconvR demuxmix DepInfeR DESeq2 Dino DMCFB dmrseq Doscheda DOTSeq dreamlet easier edge edgeR eisaR ENmix ExploreModelMatrix ExpoRiskR findIPs fishpond flowPloidy fmrs GAprediction gCrisprTools GEM GENIE3 GenomicOZone GIGSEA glmGamPoi glmSparseNet GlobalAncova globalSeq GMRP GNET2 gpls GRaNIE granulator graper gwasurvivr HiCPotts hierinf IFAA IgGeneUsage IMAS IVAS KBoost kebabs LEA lemur lfa limma limmaGUI limpa limpca LinkHD LRcell LRDE MAGAR mbQTL Melissa metaCCA metaseqR2 MethReg methylGSA methyLImp2 methylSig MetNet mirTarRnaSeq mistyR mixOmics MOSClip msqrob2 MSstatsResponse multiWGCNA NewWave OAtools omicRexposome OPWeight pairkat pathwayPCA pengls PepSetTest pmm POMA proDA protGear RankMap ResidualMatrix rifi RIVER RLassoCox RNAdecay rnaEditr roastgsa RolDE ropls rqt saseR satuRn sccomp scLANE scMET scQTLtools sevenC SIAMCAT SOMNiBUS sparsenetgls speckle spillR splineTimeR SPONGE squallms supersigs switchde tidyexposomics timeOmics topconfects tpSVG tradeSeq transformGamPoi Trendy variancePartition weitrix XAItest xcore zenith

StructuralEquationModels (1)

ASGSCA

SupportVectorMachine (11)

cellity EnMCB fgga kebabs LedPred procoil SC3 scAnnotatR scmap scReClassify sigFeature

Infrastructure (615)

affxparser affyContam affyio AllelicImbalance AnnotationFilter AnnotationForge AnnotationHub AnVIL AnVILAz AnVILBase AnVILBilling AnVILGCP AnVILPublish AnVILWorkflow aroma.light arrayMvout basecallQC BaseSpaceR basilisk basilisk.utils beachmat beachmat.hdf5 beachmat.tiledb bioassayR Biobase Bioc.gff BiocAzul BiocBaseUtils BiocBook BiocBuildReporter BiocCheck BiocFHIR BiocGenerics BiocHail BiocMaintainerApp biocmake BiocParallel BiocPkgDash BiocPkgTools biocroxytest BiocSklearn BiocVersion biocViews biodb biodbChebi BioMVCClass Biostrings biovizBase BSgenome BSgenomeForge BufferedMatrix BufferedMatrixMethods bumphunter BumpyMatrix Cardinal CardinalIO cBioPortalData CellBench CGHbase ChemmineOB ChemmineR chimeraviz ChIPseqR ChIPsim Chromatograms cigarillo convert CTDquerier cummeRbund CuratedAtlasQueryR DeeDeeExperiment DelayedArray DelayedDataFrame DelayedMatrixStats DelayedTensor DFplyr dir.expiry doseR DynDoc eiR epivizr epivizrData epivizrServer epivizrStandalone ExperimentHub ExperimentHubData ExperimentSubset fastRanges flowBeads flowcatchR flowCore flowViz fmcsR fraq GCPtools gDRimport gDRstyle gDRutils GDSArray gdsfmt genomeIntervals GenomicAlignments GenomicCoordinates GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges GenomicScores GenomicTuples GenVisR GEOmetadb ggbio ggcyto GraphExperiment h5mread HDF5Array Herper HiCBricks hmdbQuery HoloFoodR HuBMAPR HubPub Icens illuminaio imageFeatureTCGA InteractionSet IRanges iSEEde iSEEhex iSEEindex iSEEpathways koinar LoomExperiment lpsymphony LRBaseDbi MatrixGenerics matter MeSHDbi MetaboAnnotation MetaboCoreUtils MetID MGnifyR microRNA mimager Modstrings MoleculeExperiment monocle MsBackendMassbank MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendSql MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment MultimodalExperiment MVCClass mzR oligoClasses OmicsMLRepoR ontoProc OrganismDbi OSTA.data panp pdInfoBuilder PhIPData pipeFrame PlinkMatrix plyinteractions plyranges preprocessCore ProtGenerics PSMatch QFeatures QTLExperiment R453Plus1Toolbox RaggedExperiment rawDiag rawrr RBedMethyl Rcollectl rebook RedisParam ReducedExperiment Rega ReUseData rexposome rhdf5 rhdf5client rhdf5filters Rhdf5lib ribor RNAmodR RNAmodR.ML RProtoBufLib RSeqAn RTCA S4Arrays S4Vectors SCArray scater scPassport scTreeViz scviR SeqArray Seqinfo SharedObject shinybiocloader SingleCellAlleleExperiment SingleCellExperiment SNPRelate Spaniel SparseArray sparseMatrixStats SpatialExperiment SpatialExperimentIO Spectra SpectraQL SpectriPy SQLDataFrame SRAdb ssrch Structstrings SummarizedExperiment systemPipeR systemPipeShiny systemPipeTools TENxIO terraTCGAdata TFARM tidybulk tidyFlowCore tidyomics tidyprint tidySingleCellExperiment tidySpatialExperiment tidySummarizedExperiment TileDBArray tkWidgets TnT topdownr TreeSummarizedExperiment txdbmaker UCSC.utils UniProt.ws updateObject VariantExperiment VCFArray VisiumIO weaver webbioc widgetTools XeniumIO xenLite XVector ZarrArray

DataImport (340)

aCGH affxparser affyio affylmGUI 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 AlpsNMR AMARETTO anndataR AnnotationHub AnnotationHubData AnVILGCP APAlyzer ArrayExpress ASICS assorthead autonomics bamsignals bandle basecallQC BaseSpaceR Basic4Cseq BayesSpace beachmat beachmat.hdf5 beachmat.tiledb bedbaser BgeeDB bigmelon BindingSiteFinder bioassayR biobroom Bioc.gff BiocAzul BiocFHIR BiocFileCache BiocIO biodb biodbChebi biomformat BioNet Biostrings biscuiteer brendaDb BSgenomeForge bugsigdbr CAGEfightR CardinalIO CATALYST cbpManager celda cellmigRation cellxgenedp ChemmineOB ChemmineR chevreulPlot chevreulProcess chevreulShiny chihaya ChIPanalyser chipseq ClonalSim cmapR CNEr CNVfilteR codelink cogena CONFESS CopyNumberPlots CoSIA ctc CTdata CTDquerier CTexploreR cummeRbund cypress cytolib cytomapper cytoMEM CytoML cytoviewer DAPAR DECIPHER deepSNV DegNorm dittoSeq DMRcate DNEA Doscheda DropletUtils DspikeIn easylift edge eiR ENmix ExperimentHub ExperimentHubData ExperimentSubset faers FLAMES flowGate flowSpecs flowTime flowWorkspace fmcsR GCPtools gDR gDRimport gdsfmt gemini gemma.R GeneRegionScan genomeIntervals GenomicAlignments GenomicDataCommons GenomicFiles GenomicInteractions GEOfastq GeomxTools GEOquery ggkegg ggtree GraphExperiment Guitar gypsum h5mread HDF5Array hdxmsqc HelloRanges HELP HicAggR HiCaptuRe HiCBricks HiCExperiment HiCool HiCParser HiCPotts HoloFoodR hpar HTqPCR HuBMAPR HubPub ibh illuminaio imageFeatureTCGA imcRtools IONiseR ISAnalytics iscream iSEEhub iSEEtree IsoformSwitchAnalyzeR IWTomics karyoploteR KnowSeq limma limmaGUI limpa LOBSTAHS LoomExperiment MACSQuantifyR MAGAR makecdfenv MANOR MassArray matter MDTS megadepth memes metabom8 metaseqR2 MethTargetedNGS MGnifyR mia miaDash minfi mitch mitoClone2 Modstrings MoleculeExperiment monocle motifStack MsBackendMassbank MsBackendMetaboLights MsBackendMgf MsBackendMsp MsBackendSql MsExperiment msgbsR MSnbase MSstatsConvert MuData muscle mzID mzR NanoMethViz NanoStringNCTools ncRNAtools ndexr normr notame notameStats notameViz nucleR OAtools oligo OmnipathR ompBAM openCyto ORFik OSTA.data OTUbase PepsNMR periodicDNA pfamAnalyzeR pgxRpi plotGrouper podkat profileplyr ProteoDisco puma qPLEXanalyzer QSutils QTLExperiment queeems R453Plus1Toolbox R4RNA Rarr RBedMethyl RBioFormats rBLAST Rcpi RcwlPipelines RCX ReadqPCR recount recount3 recoup REMP ReUseData rexposome rfaRm rhdf5 rhdf5client rhdf5filters Rhtslib RiboDiPA RImmPort rmspc RnBeads roastgsa rpx Rqc Rsamtools RTCGA Rtpca rtracklayer Scale4C SCArray SCArray.sat scater scCB2 scDataviz scGPS schex scmap SCOPE scoup scPassport scPipe scuttle scviR seahtrue segmentSeq sevenbridges sevenC ShortRead SICtools SimFFPE simPIC SingleCellAlleleExperiment SingleCellExperiment singleCellTK SiPSiC sitadela snapcount SpaceTrooper Spaniel spARI SpatialArtifacts SpatialExperiment SpatialExperimentIO SpatialOmicsOverlay SPIAT SpotClean SRAdb stPipe Structstrings StructuralVariantAnnotation SurfR svaNUMT svaRetro SynExtend systemPipeR systemPipeShiny systemPipeTools tanggle TCGAutils TENxIO terraTCGAdata TPP2D transomics2cytoscape traseR treeio tRNAdbImport tRNAscanImport TRONCO TVTB txdbmaker tximeta tximport UCSC.utils universalmotif VariantAnnotation VisiumIO visiumStitched XeniumIO ZarrArray zellkonverter

DataRepresentation (160)

alabaster alabaster.base alabaster.bumpy alabaster.files alabaster.mae alabaster.matrix alabaster.ranges alabaster.sce alabaster.schemas alabaster.se alabaster.sfe alabaster.spatial alabaster.string alabaster.vcf anndataR assorthead BaseSpaceR beachmat beachmat.hdf5 beachmat.tiledb bioCancer BiocFHIR Biostrings BSgenome BSgenomeForge BumpyMatrix CAGEfightR cbpManager cellmigRation CellTrails chihaya chromPlot cmapR cogena consensus CrispRVariants CTDquerier cummeRbund cytolib cytoMEM CytoML DeeDeeExperiment DelayedArray DelayedDataFrame DelayedMatrixStats DelayedRandomArray DelayedTensor DepecheR DFplyr doseR esetVis ExperimentSubset flowDensity flowPlots flowSpecs flowWorkspace GA4GHclient GDSArray GenomeInfoDb GenomicCoordinates GenomicDistributions GenomicInteractions GenomicRanges GenomicTuples GenVisR GloScope GOexpress GraphExperiment gVenn h5mread HDF5Array HicAggR ILoReg imageFeatureTCGA InteractionSet ipdDb IRanges KEGGlincs linkSet looking4clusters LoomExperiment MACSQuantifyR maftools matter Modstrings MoleculeExperiment monocle MultiAssayExperiment MultiBaC MultiDataSet MultimodalExperiment omicsGMF OmicsMLRepoR OMICsPCA Omixer OmnipathR omXplore openCyto oposSOM OSAT OSTA.data Pedixplorer phantasus PhIPData PhyloProfile pipeComp plyranges QTLExperiment R453Plus1Toolbox R4RNA RaggedExperiment rBiopaxParser Rcpi ReducedExperiment ReportingTools ResidualMatrix rexposome RImmPort RTCGA Rvisdiff S4Arrays S4Vectors SC3 ScaledMatrix SCArray SCArray.sat scater scmap seahtrue SeqArray Seqinfo SETA SingleCellAlleleExperiment SingleCellExperiment Spaniel SparseArray sparseMatrixStats SpatialExperiment SpatialExperimentIO SpatialFeatureExperiment spatialHeatmap SpatialOmicsOverlay SplicingGraphs SQLDataFrame Structstrings surfaltr TileDBArray TreeAndLeaf treeio TreeSummarizedExperiment TVTB Ularcirc updateObject VariantExperiment VCFArray VennDetail weitrix XVector ZarrArray zellkonverter

GPU (1)

COTAN

AnnotationData (928)

Organism (667)

AlphaMissense.v2023.hg19 AlphaMissense.v2023.hg38 BioMartGOGeneSets cadd.v1.6.hg19 cadd.v1.6.hg38 EpiTxDb.Hs.hg38 EpiTxDb.Mm.mm10 EpiTxDb.Sc.sacCer3 GeneSummary GenomeInfoDbData phastCons35way.UCSC.mm39 phyloP35way.UCSC.mm39 TxDb.Athaliana.BioMart.plantsmart51 UniProtKeywords

Anopheles_gambiae (4)

anopheles.db0 org.Ag.eg.db plasmodiumanophelescdf plasmodiumanophelesprobe

Apis_mellifera (4)

BSgenome.Amellifera.BeeBase.assembly4 BSgenome.Amellifera.NCBI.AmelHAv3.1 BSgenome.Amellifera.UCSC.apiMel2 BSgenome.Amellifera.UCSC.apiMel2.masked

Arabidopsis_lyrata

Arabidopsis_thaliana (15)

ag.db agcdf agprobe arabidopsis.db0 ath1121501.db ath1121501cdf ath1121501frmavecs ath1121501probe BSgenome.Athaliana.TAIR.04232008 BSgenome.Athaliana.TAIR.TAIR9 org.At.tair.db TxDb.Athaliana.BioMart.plantsmart22 TxDb.Athaliana.BioMart.plantsmart25 TxDb.Athaliana.BioMart.plantsmart28 TxDb.Athaliana.BioMart.plantsmart51

Asparagus_officinalis (1)

BSgenome.Aofficinalis.NCBI.V1

Bacillus_subtilis (2)

bsubtiliscdf bsubtilisprobe

Bos_taurus (16)

bovine.db bovine.db0 bovinecdf bovineprobe BSgenome.Btaurus.UCSC.bosTau3 BSgenome.Btaurus.UCSC.bosTau3.masked BSgenome.Btaurus.UCSC.bosTau4 BSgenome.Btaurus.UCSC.bosTau4.masked BSgenome.Btaurus.UCSC.bosTau6 BSgenome.Btaurus.UCSC.bosTau6.masked BSgenome.Btaurus.UCSC.bosTau8 BSgenome.Btaurus.UCSC.bosTau9 BSgenome.Btaurus.UCSC.bosTau9.masked org.Bt.eg.db TxDb.Btaurus.UCSC.bosTau8.refGene TxDb.Btaurus.UCSC.bosTau9.refGene

Caenorhabditis_elegans (12)

BSgenome.Celegans.UCSC.ce10 BSgenome.Celegans.UCSC.ce11 BSgenome.Celegans.UCSC.ce2 BSgenome.Celegans.UCSC.ce6 celegans.db celeganscdf celegansprobe org.Ce.eg.db TxDb.Celegans.UCSC.ce11.ensGene TxDb.Celegans.UCSC.ce11.refGene TxDb.Celegans.UCSC.ce6.ensGene worm.db0

Callithrix_jacchus (2)

BSgenome.Cjacchus.UCSC.calJac3 BSgenome.Cjacchus.UCSC.calJac4

Canis_familiaris (16)

BSgenome.Cfamiliaris.UCSC.canFam2 BSgenome.Cfamiliaris.UCSC.canFam2.masked BSgenome.Cfamiliaris.UCSC.canFam3 BSgenome.Cfamiliaris.UCSC.canFam3.masked canine.db canine.db0 canine2.db canine2cdf canine2probe caninecdf canineprobe org.Cf.eg.db TxDb.Cfamiliaris.UCSC.canFam3.refGene TxDb.Cfamiliaris.UCSC.canFam4.refGene TxDb.Cfamiliaris.UCSC.canFam5.refGene TxDb.Cfamiliaris.UCSC.canFam6.refGene

Cicer_arietinum (1)

BSgenome.Carietinum.NCBI.v1

Ciona_intestinalis

Chlamydomonas_reinhardtii (1)

BSgenome.Creinhardtii.JGI.v5.6

Danio_rerio (15)

BSgenome.Drerio.UCSC.danRer10 BSgenome.Drerio.UCSC.danRer11 BSgenome.Drerio.UCSC.danRer5 BSgenome.Drerio.UCSC.danRer5.masked BSgenome.Drerio.UCSC.danRer6 BSgenome.Drerio.UCSC.danRer6.masked BSgenome.Drerio.UCSC.danRer7 BSgenome.Drerio.UCSC.danRer7.masked org.Dr.eg.db TxDb.Drerio.UCSC.danRer10.refGene TxDb.Drerio.UCSC.danRer11.refGene zebrafish.db zebrafish.db0 zebrafishcdf zebrafishprobe

Drosophila_melanogaster (17)

BSgenome.Dmelanogaster.UCSC.dm2 BSgenome.Dmelanogaster.UCSC.dm2.masked BSgenome.Dmelanogaster.UCSC.dm3 BSgenome.Dmelanogaster.UCSC.dm3.masked BSgenome.Dmelanogaster.UCSC.dm6 drosgenome1.db drosgenome1cdf drosgenome1probe drosophila2.db drosophila2cdf drosophila2probe fly.db0 indac.db org.Dm.eg.db rGenomeTracksData TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Dmelanogaster.UCSC.dm6.ensGene

Drosophila_virilis (1)

BSgenome.Dvirilis.Ensembl.dvircaf1

Eremothecium_gossypii

Escherichia_coli (12)

BSgenome.Ecoli.NCBI.20080805 ecoli2.db ecoli2cdf ecoli2probe ecoliasv2cdf ecoliasv2probe ecolicdf ecoliK12.db0 ecoliprobe ecoliSakai.db0 org.EcK12.eg.db org.EcSakai.eg.db

Gallus_gallus (14)

BSgenome.Ggallus.UCSC.galGal3 BSgenome.Ggallus.UCSC.galGal3.masked BSgenome.Ggallus.UCSC.galGal4 BSgenome.Ggallus.UCSC.galGal4.masked BSgenome.Ggallus.UCSC.galGal5 BSgenome.Ggallus.UCSC.galGal6 chicken.db chicken.db0 chickencdf chickenprobe org.Gg.eg.db TxDb.Ggallus.UCSC.galGal4.refGene TxDb.Ggallus.UCSC.galGal5.refGene TxDb.Ggallus.UCSC.galGal6.refGene

Gasterosteus_aculeatus (2)

BSgenome.Gaculeatus.UCSC.gasAcu1 BSgenome.Gaculeatus.UCSC.gasAcu1.masked

Glycine_max (1)

BSgenome.Gmax.NCBI.Gmv40

Homo_sapiens (254)

Hordeum_vulgare (2)

barley1cdf barley1probe

Kluyveromyces_lactis

Macaca_fascicularis (2)

BSgenome.Mfascicularis.NCBI.5.0 BSgenome.Mfascicularis.NCBI.6.0

Macaca_mulatta (12)

BSgenome.Mmulatta.UCSC.rheMac10 BSgenome.Mmulatta.UCSC.rheMac2 BSgenome.Mmulatta.UCSC.rheMac2.masked BSgenome.Mmulatta.UCSC.rheMac3 BSgenome.Mmulatta.UCSC.rheMac3.masked BSgenome.Mmulatta.UCSC.rheMac8 org.Mmu.eg.db rhesuscdf rhesusprobe TxDb.Mmulatta.UCSC.rheMac10.refGene TxDb.Mmulatta.UCSC.rheMac3.refGene TxDb.Mmulatta.UCSC.rheMac8.refGene

Magnaporthe_grisea

Medicago_truncatula

Monodelphis_domestica (1)

BSgenome.Mdomestica.UCSC.monDom5

Mus_musculus (117)

BSgenome.Mmusculus.UCSC.mm10 BSgenome.Mmusculus.UCSC.mm10.masked BSgenome.Mmusculus.UCSC.mm39 BSgenome.Mmusculus.UCSC.mm8 BSgenome.Mmusculus.UCSC.mm8.masked BSgenome.Mmusculus.UCSC.mm9 BSgenome.Mmusculus.UCSC.mm9.masked chromhmmData clariomsmousehttranscriptcluster.db clariomsmousetranscriptcluster.db ENCODExplorerData EnsDb.Mmusculus.v75 EnsDb.Mmusculus.v79 EpiTxDb.Mm.mm10 htmg430a.db htmg430acdf htmg430aprobe htmg430b.db htmg430bcdf htmg430bprobe htmg430pm.db htmg430pmcdf htmg430pmprobe illuminaMousev1.db illuminaMousev1p1.db illuminaMousev2.db lumiMouseAll.db m10kcod.db m20kcod.db mgu74a.db mgu74acdf mgu74aprobe mgu74av2.db mgu74av2cdf mgu74av2probe mgu74b.db mgu74bcdf mgu74bprobe mgu74bv2.db mgu74bv2cdf mgu74bv2probe mgu74c.db mgu74ccdf mgu74cprobe mgu74cv2.db mgu74cv2cdf mgu74cv2probe mguatlas5k.db mgug4104a.db mgug4120a.db mgug4121a.db mgug4122a.db mi16cod.db mm24kresogen.db MmAgilentDesign026655.db moe430a.db moe430acdf moe430aprobe moe430b.db moe430bcdf moe430bprobe moex10stprobeset.db moex10sttranscriptcluster.db mogene10stprobeset.db mogene10sttranscriptcluster.db mogene10stv1cdf mogene10stv1probe mogene11stprobeset.db mogene11sttranscriptcluster.db mogene20stprobeset.db mogene20sttranscriptcluster.db mogene21stprobeset.db mogene21sttranscriptcluster.db mouse.db0 mouse4302.db mouse4302cdf mouse4302frmavecs mouse4302probe mouse430a2.db mouse430a2cdf mouse430a2frmavecs mouse430a2probe mouseCHRLOC mpedbarray.db mta10probeset.db mta10transcriptcluster.db mu11ksuba.db mu11ksubacdf mu11ksubaprobe mu11ksubb.db mu11ksubbcdf mu11ksubbprobe Mu15v1.db mu19ksuba.db mu19ksubacdf mu19ksubb.db mu19ksubbcdf mu19ksubc.db mu19ksubccdf Mu22v3.db mu6500subacdf mu6500subbcdf mu6500subccdf mu6500subdcdf Mus.musculus mwgcod.db nugomm1a520177.db nugomm1a520177cdf nugomm1a520177probe org.Mm.eg.db phastCons35way.UCSC.mm39 phyloP35way.UCSC.mm39 TxDb.Mmusculus.UCSC.mm10.ensGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm39.knownGene TxDb.Mmusculus.UCSC.mm39.refGene TxDb.Mmusculus.UCSC.mm9.knownGene

Neurospora_crassa

Oncorhynchus_mykiss

Oryza_sativa (1)

BSgenome.Osativa.MSU.MSU7

Pan_paniscus (2)

BSgenome.Ppaniscus.UCSC.panPan1 BSgenome.Ppaniscus.UCSC.panPan2

Pan_troglodytes (11)

BSgenome.Ptroglodytes.UCSC.panTro2 BSgenome.Ptroglodytes.UCSC.panTro2.masked BSgenome.Ptroglodytes.UCSC.panTro3 BSgenome.Ptroglodytes.UCSC.panTro3.masked BSgenome.Ptroglodytes.UCSC.panTro5 BSgenome.Ptroglodytes.UCSC.panTro6 chimp.db0 org.Pt.eg.db TxDb.Ptroglodytes.UCSC.panTro4.refGene TxDb.Ptroglodytes.UCSC.panTro5.refGene TxDb.Ptroglodytes.UCSC.panTro6.refGene

Plasmodium_falciparum (4)

malaria.db0 org.Pf.plasmo.db plasmodiumanophelescdf plasmodiumanophelesprobe

Pseudomonas_aeruginosa (2)

paeg1acdf paeg1aprobe

Rattus_norvegicus (78)

Saccharomyces_cerevisiae (18)

BSgenome.Scerevisiae.UCSC.sacCer1 BSgenome.Scerevisiae.UCSC.sacCer2 BSgenome.Scerevisiae.UCSC.sacCer3 EpiTxDb.Sc.sacCer3 org.Sc.sgd.db TxDb.Scerevisiae.UCSC.sacCer2.sgdGene TxDb.Scerevisiae.UCSC.sacCer3.sgdGene ye6100subacdf ye6100subbcdf ye6100subccdf ye6100subdcdf yeast.db0 yeast2.db yeast2cdf yeast2probe ygs98.db ygs98cdf ygs98probe

Saccharum_officinarum (2)

sugarcanecdf sugarcaneprobe

Salmo_salar

Schizosaccharomyces_pombe

Staphylococcus_aureus (2)

saureuscdf saureusprobe

Sus_scrofa (10)

BSgenome.Sscrofa.UCSC.susScr11 BSgenome.Sscrofa.UCSC.susScr3 BSgenome.Sscrofa.UCSC.susScr3.masked org.Ss.eg.db pig.db0 porcine.db porcinecdf porcineprobe TxDb.Sscrofa.UCSC.susScr11.refGene TxDb.Sscrofa.UCSC.susScr3.refGene

Taeniopygia_guttata (3)

BSgenome.Tguttata.UCSC.taeGut1 BSgenome.Tguttata.UCSC.taeGut1.masked BSgenome.Tguttata.UCSC.taeGut2

Toxoplasma_gondii (1)

BSgenome.Tgondii.ToxoDB.7.0

Triticum_aestivum

Vitis_vinifera (5)

BSgenome.Vvinifera.URGI.IGGP12Xv0 BSgenome.Vvinifera.URGI.IGGP12Xv2 BSgenome.Vvinifera.URGI.IGGP8X vitisviniferacdf vitisviniferaprobe

Xenopus_laevis (3)

org.Xl.eg.db xenopus.db0 xlaevis.db

Xenopus_tropicalis (1)

xtropicalisprobe

Zea_mays (2)

maizecdf maizeprobe

ChipManufacturer (402)

AffymetrixChip (342)

AgilentChip (15)

hgug4100a.db hgug4101a.db hgug4110b.db hgug4111a.db hgug4112a.db HsAgilentDesign026652.db mgug4104a.db mgug4120a.db mgug4121a.db mgug4122a.db MmAgilentDesign026655.db rgug4105a.db rgug4130a.db rgug4131a.db RnAgilentDesign028282.db

ClonetechChip

GEChip

INDACChip (1)

indac.db

QiagenChip (1)

hguqiagenv3.db

RNG_MRCChip (2)

hs25kresogen.db mm24kresogen.db

RocheChip

UniversityHealthNetwork

CodelinkChip (12)

adme16cod.db h10kcod.db h20kcod.db hi16cod.db hwgcod.db m10kcod.db m20kcod.db mi16cod.db mwgcod.db r10kcod.db ri16cod.db rwgcod.db

CustomCDF

GACustomCDF

MBNICustomCDF

CustomArray (2)

hgubeta7.db hguDKFZ31.db

CustomDBSchema (10)

AHPathbankDbs AHWikipathwaysDbs ChemmineDrugs ENCODExplorerData hpAnnot metaboliteIDmapping RmiR.Hs.miRNA RmiR.hsa synaptome.data synaptome.db

GeneCardsCustomSchema

SequenceAnnotation (4)

LymphoSeqDB

GenomicSequence (4)

CTCF excluderanges LymphoSeqDB TENET.AnnotationHub

ChipName (197)

adme16cod.db ag.db agcdf agprobe ath1121501.db ath1121501cdf ath1121501frmavecs ath1121501probe celegans.db celeganscdf celegansprobe drosgenome1.db drosgenome1cdf drosgenome1probe drosophila2.db drosophila2cdf drosophila2probe h10kcod.db h20kcod.db hcg110.db hcg110cdf hcg110probe hgfocus.db hgfocuscdf hgfocusprobe hgu133a.db hgu133a2.db hgu133a2cdf hgu133a2frmavecs hgu133a2probe hgu133acdf hgu133afrmavecs hgu133aprobe hgu133b.db hgu133bcdf hgu133bprobe hgu133plus2.db hgu133plus2cdf hgu133plus2frmavecs hgu133plus2probe hgu95a.db hgu95acdf hgu95aprobe hgu95av2 hgu95av2.db hgu95av2cdf hgu95av2probe hgu95b.db hgu95bcdf hgu95bprobe hgu95c.db hgu95ccdf hgu95cprobe hgu95d.db hgu95dcdf hgu95dprobe hgu95e.db hgu95ecdf hgu95eprobe hguatlas13k.db hgug4100a.db hgug4101a.db hgug4110b.db hgug4111a.db hgug4112a.db hguqiagenv3.db hi16cod.db hs25kresogen.db hu35ksuba.db hu35ksubacdf hu35ksubaprobe hu35ksubb.db hu35ksubbcdf hu35ksubbprobe hu35ksubc.db hu35ksubccdf hu35ksubcprobe hu35ksubd.db hu35ksubdcdf hu35ksubdprobe hu6800.db hu6800cdf hu6800probe HuO22.db hwgcod.db illuminaHumanv1.db illuminaHumanv2.db illuminaMousev1.db illuminaMousev1p1.db illuminaRatv1.db indac.db m10kcod.db m20kcod.db mgu74a.db mgu74acdf mgu74aprobe mgu74av2.db mgu74av2cdf mgu74av2probe mgu74b.db mgu74bcdf mgu74bprobe mgu74bv2.db mgu74bv2cdf mgu74bv2probe mgu74c.db mgu74ccdf mgu74cprobe mgu74cv2.db mgu74cv2cdf mgu74cv2probe mguatlas5k.db mgug4121a.db mgug4122a.db mi16cod.db mm24kresogen.db moe430a.db moe430acdf moe430aprobe moe430b.db moe430bcdf moe430bprobe mouse4302.db mouse4302cdf mouse4302frmavecs mouse4302probe mouse430a2.db mouse430a2cdf mouse430a2frmavecs mouse430a2probe mpedbarray.db mu11ksuba.db mu11ksubacdf mu11ksubaprobe mu11ksubb.db mu11ksubbcdf mu11ksubbprobe Mu15v1.db mu19ksuba.db mu19ksubacdf mu19ksubb.db mu19ksubbcdf mu19ksubc.db mu19ksubccdf Mu22v3.db mwgcod.db Norway981.db OperonHumanV3.db PartheenMetaData.db pedbarrayv10.db pedbarrayv9.db r10kcod.db rae230a.db rae230acdf rae230aprobe rae230b.db rae230bcdf rae230bprobe rat2302.db rat2302cdf rat2302frmavecs rat2302probe rgu34a.db rgu34acdf rgu34aprobe rgu34b.db rgu34bcdf rgu34bprobe rgu34c.db rgu34ccdf rgu34cprobe rgug4130a.db ri16cod.db rnu34.db rnu34cdf rnu34probe Roberts2005Annotation.db rtu34.db rtu34cdf rtu34probe rwgcod.db SHDZ.db u133x3p.db u133x3pcdf u133x3pprobe xenopuslaeviscdf xenopuslaevisprobe yeast2.db yeast2cdf yeast2probe ygs98.db ygs98cdf ygs98frmavecs ygs98probe zebrafish.db zebrafishcdf zebrafishprobe

adme16cod (1)

adme16cod.db

ag (3)

ag.db agcdf agprobe

ath1121501 (4)

ath1121501.db ath1121501cdf ath1121501frmavecs ath1121501probe

celegans (3)

celegans.db celeganscdf celegansprobe

drosgenome1 (3)

drosgenome1.db drosgenome1cdf drosgenome1probe

drosophila2 (3)

drosophila2.db drosophila2cdf drosophila2probe

h10kcod (1)

h10kcod.db

h20kcod (1)

h20kcod.db

hcg110 (3)

hcg110.db hcg110cdf hcg110probe

hgfocus (3)

hgfocus.db hgfocuscdf hgfocusprobe

hgu133a2 (4)

hgu133a2.db hgu133a2cdf hgu133a2frmavecs hgu133a2probe

hgu133a (4)

hgu133a.db hgu133acdf hgu133afrmavecs hgu133aprobe

hgu133b (3)

hgu133b.db hgu133bcdf hgu133bprobe

hgu133plus2 (4)

hgu133plus2.db hgu133plus2cdf hgu133plus2frmavecs hgu133plus2probe

hgu95a (3)

hgu95a.db hgu95acdf hgu95aprobe

hgu95av2 (4)

hgu95av2 hgu95av2.db hgu95av2cdf hgu95av2probe

hgu95b (3)

hgu95b.db hgu95bcdf hgu95bprobe

hgu95c (3)

hgu95c.db hgu95ccdf hgu95cprobe

hgu95d (3)

hgu95d.db hgu95dcdf hgu95dprobe

hgu95e (3)

hgu95e.db hgu95ecdf hgu95eprobe

hguatlas13k (1)

hgug4100a (1)

hgug4101a (1)

hgug4110b (1)

hgug4111a (1)

hgug4112a (1)

hguqiagenv3 (1)

hi16cod (1)

hs25kresogen (1)

hu35ksuba (3)

hu35ksuba.db hu35ksubacdf hu35ksubaprobe

hu35ksubb (3)

hu35ksubb.db hu35ksubbcdf hu35ksubbprobe

hu35ksubc (3)

hu35ksubc.db hu35ksubccdf hu35ksubcprobe

hu35ksubd (3)

hu35ksubd.db hu35ksubdcdf hu35ksubdprobe

hu6800 (3)

hu6800.db hu6800cdf hu6800probe

HuO22 (1)

hwgcod (1)

indac (1)

illuminaHumanv1 (1)

illuminaHumanv2 (1)

illuminaMousev1 (1)

illuminaMousev1p1 (1)

illuminaMousev1p1.db

illuminaRatv1 (1)

illuminaRatv1.db

JazaerimetaData

lumiHumanV1

lumiMouseV1

lumiHumanV2

lumiRatV1

m10kcod (1)

m20kcod (1)

mi16cod (1)

mm24kresogen (1)

mgu74a (3)

mgu74a.db mgu74acdf mgu74aprobe

mgu74av2 (3)

mgu74av2.db mgu74av2cdf mgu74av2probe

mgu74b (3)

mgu74b.db mgu74bcdf mgu74bprobe

mgu74bv2 (3)

mgu74bv2.db mgu74bv2cdf mgu74bv2probe

mgu74c (3)

mgu74c.db mgu74ccdf mgu74cprobe

mgu74cv2 (3)

mgu74cv2.db mgu74cv2cdf mgu74cv2probe

mguatlas5k (1)

mguatlas5k.db

mgug4121a (1)

mgug4121a.db

mgug4122a (1)

mgug4122a.db

moe430a (3)

moe430a.db moe430acdf moe430aprobe

moe430b (3)

moe430b.db moe430bcdf moe430bprobe

mouse4302 (4)

mouse4302.db mouse4302cdf mouse4302frmavecs mouse4302probe

mouse430a2 (4)

mouse430a2.db mouse430a2cdf mouse430a2frmavecs mouse430a2probe

mpedbarray (1)

mpedbarray.db

mu11ksuba (3)

mu11ksuba.db mu11ksubacdf mu11ksubaprobe

mu11ksubb (3)

mu11ksubb.db mu11ksubbcdf mu11ksubbprobe

mu19ksuba (2)

mu19ksuba.db mu19ksubacdf

mu19ksubb (2)

mu19ksubb.db mu19ksubbcdf

mu19ksubc (2)

mu19ksubc.db mu19ksubccdf

Mu15v1 (1)

Mu22v3 (1)

mwgcod (1)

Norway981 (1)

OperonHumanV3 (1)

pedbarrayv9 (1)

pedbarrayv10 (1)

PartheenMetaData (1)

r10kcod (1)

rae230a (3)

rae230a.db rae230acdf rae230aprobe

rae230b (3)

rae230b.db rae230bcdf rae230bprobe

rat2302 (4)

rat2302.db rat2302cdf rat2302frmavecs rat2302probe

rgu34a (3)

rgu34a.db rgu34acdf rgu34aprobe

rgu34b (3)

rgu34b.db rgu34bcdf rgu34bprobe

rgu34c (3)

rgu34c.db rgu34ccdf rgu34cprobe

rgug4130a (1)

rgug4130a.db

ri16cod (1)

ri16cod.db

rnu34 (3)

rnu34.db rnu34cdf rnu34probe

Roberts2005Annotation (1)

Roberts2005Annotation.db

rtu34 (3)

rtu34.db rtu34cdf rtu34probe

rwgcod (1)

rwgcod.db

SHDZ (1)

SHDZ.db

u133x3p (3)

u133x3p.db u133x3pcdf u133x3pprobe

xenopuslaevis (2)

xenopuslaeviscdf xenopuslaevisprobe

yeast2 (3)

yeast2.db yeast2cdf yeast2probe

ygs98 (4)

ygs98.db ygs98cdf ygs98frmavecs ygs98probe

zebrafish (3)

zebrafish.db zebrafishcdf zebrafishprobe

hcgi12k

hcgi8k

PackageType (654)

AlphaMissense.v2023.hg19 AlphaMissense.v2023.hg38 cadd.v1.6.hg19 cadd.v1.6.hg38 hpAnnot phastCons35way.UCSC.mm39 phyloP35way.UCSC.mm39 rat2302frmavecs

BSgenome (111)

cdf (118)

agcdf ath1121501cdf barley1cdf bovinecdf bsubtiliscdf canine2cdf caninecdf celeganscdf chickencdf citruscdf cottoncdf cyp450cdf drosgenome1cdf drosophila2cdf ecoli2cdf ecoliasv2cdf ecolicdf gp53cdf hcg110cdf hgfocuscdf hgu133a2cdf hgu133acdf hgu133atagcdf hgu133bcdf hgu133plus2cdf hgu219cdf hgu95acdf hgu95av2cdf hgu95bcdf hgu95ccdf hgu95dcdf hgu95ecdf hivprtplus2cdf Hspec hspeccdf hthgu133acdf hthgu133bcdf hthgu133pluspmcdf htmg430acdf htmg430bcdf htmg430pmcdf htrat230pmcdf htratfocuscdf hu35ksubacdf hu35ksubbcdf hu35ksubccdf hu35ksubdcdf hu6800cdf hu6800subacdf hu6800subbcdf hu6800subccdf hu6800subdcdf hugene10stv1cdf maizecdf medicagocdf mgu74acdf mgu74av2cdf mgu74bcdf mgu74bv2cdf mgu74ccdf mgu74cv2cdf mirna102xgaincdf mirna10cdf mirna20cdf moe430acdf moe430bcdf mogene10stv1cdf mouse4302cdf mouse430a2cdf mu11ksubacdf mu11ksubbcdf mu19ksubacdf mu19ksubbcdf mu19ksubccdf mu6500subacdf mu6500subbcdf mu6500subccdf mu6500subdcdf nugohs1a520180cdf nugomm1a520177cdf paeg1acdf plasmodiumanophelescdf poplarcdf porcinecdf primeviewcdf rae230acdf rae230bcdf ragene10stv1cdf rat2302cdf rattoxfxcdf rgu34acdf rgu34bcdf rgu34ccdf rhesuscdf ricecdf rnu34cdf rtu34cdf saureuscdf soybeancdf sugarcanecdf test1cdf test2cdf test3cdf tomatocdf u133aaofav2cdf u133x3pcdf vitisviniferacdf wheatcdf xenopuslaeviscdf xlaevis2cdf xtropicaliscdf ye6100subacdf ye6100subbcdf ye6100subccdf ye6100subdcdf yeast2cdf ygs98cdf zebrafishcdf

ChipDb (176)

db0 (19)

anopheles.db0 arabidopsis.db0 bovine.db0 canine.db0 chicken.db0 chimp.db0 ecoliK12.db0 ecoliSakai.db0 fly.db0 human.db0 malaria.db0 mouse.db0 pig.db0 rat.db0 rhesus.db0 worm.db0 xenopus.db0 yeast.db0 zebrafish.db0

InparanoidDb

OrganismDb (3)

Homo.sapiens Mus.musculus Rattus.norvegicus

PolyPhen

probe (98)

agprobe ath1121501probe barley1probe bovineprobe bsubtilisprobe canine2probe canineprobe celegansprobe chickenprobe citrusprobe cottonprobe drosgenome1probe drosophila2probe ecoli2probe ecoliasv2probe ecoliprobe EPICv2manifest hcg110probe hgfocusprobe hgu133a2probe hgu133aprobe hgu133atagprobe hgu133bprobe hgu133plus2probe hgu219probe hgu95aprobe hgu95av2probe hgu95bprobe hgu95cprobe hgu95dprobe hgu95eprobe hthgu133aprobe hthgu133bprobe hthgu133pluspmprobe htmg430aprobe htmg430bprobe htmg430pmprobe htrat230pmprobe htratfocusprobe hu35ksubaprobe hu35ksubbprobe hu35ksubcprobe hu35ksubdprobe hu6800probe HuExExonProbesetLocation hugene10stv1probe maizeprobe medicagoprobe mgu74aprobe mgu74av2probe mgu74bprobe mgu74bv2probe mgu74cprobe mgu74cv2probe mirna10probe moe430aprobe moe430bprobe MoExExonProbesetLocation mogene10stv1probe mouse4302probe mouse430a2probe mu11ksubaprobe mu11ksubbprobe nugohs1a520180probe nugomm1a520177probe paeg1aprobe plasmodiumanophelesprobe poplarprobe porcineprobe primeviewprobe rae230aprobe rae230bprobe RaExExonProbesetLocation ragene10stv1probe rat2302frmavecs rat2302probe rattoxfxprobe rgu34aprobe rgu34bprobe rgu34cprobe rhesusprobe riceprobe rnu34probe rtu34probe saureusprobe soybeanprobe sugarcaneprobe test3probe tomatoprobe u133x3pprobe vitisviniferaprobe wheatprobe xenopuslaevisprobe xlaevis2probe xtropicalisprobe yeast2probe ygs98probe zebrafishprobe

SIFT

SNPlocs (6)

SNPlocs.Hsapiens.dbSNP144.GRCh37 SNPlocs.Hsapiens.dbSNP144.GRCh38 SNPlocs.Hsapiens.dbSNP149.GRCh38 SNPlocs.Hsapiens.dbSNP150.GRCh38 SNPlocs.Hsapiens.dbSNP155.GRCh37 SNPlocs.Hsapiens.dbSNP155.GRCh38

XtraSNPlocs (2)

XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 XtraSNPlocs.Hsapiens.dbSNP144.GRCh38

TxDb (50)

FDb.UCSC.tRNAs GenomicState TxDb.Athaliana.BioMart.plantsmart22 TxDb.Athaliana.BioMart.plantsmart25 TxDb.Athaliana.BioMart.plantsmart28 TxDb.Athaliana.BioMart.plantsmart51 TxDb.Btaurus.UCSC.bosTau8.refGene TxDb.Btaurus.UCSC.bosTau9.refGene TxDb.Celegans.UCSC.ce11.ensGene TxDb.Celegans.UCSC.ce11.refGene TxDb.Celegans.UCSC.ce6.ensGene TxDb.Cfamiliaris.UCSC.canFam3.refGene TxDb.Cfamiliaris.UCSC.canFam4.refGene TxDb.Cfamiliaris.UCSC.canFam5.refGene TxDb.Cfamiliaris.UCSC.canFam6.refGene TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Dmelanogaster.UCSC.dm6.ensGene TxDb.Drerio.UCSC.danRer10.refGene TxDb.Drerio.UCSC.danRer11.refGene TxDb.Ggallus.UCSC.galGal4.refGene TxDb.Ggallus.UCSC.galGal5.refGene TxDb.Ggallus.UCSC.galGal6.refGene TxDb.Hsapiens.BioMart.igis TxDb.Hsapiens.UCSC.hg18.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts TxDb.Hsapiens.UCSC.hg19.refGene TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Hsapiens.UCSC.hg38.refGene TxDb.Mmulatta.UCSC.rheMac10.refGene TxDb.Mmulatta.UCSC.rheMac3.refGene TxDb.Mmulatta.UCSC.rheMac8.refGene TxDb.Mmusculus.UCSC.mm10.ensGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Mmusculus.UCSC.mm39.knownGene TxDb.Mmusculus.UCSC.mm39.refGene TxDb.Mmusculus.UCSC.mm9.knownGene TxDb.Ptroglodytes.UCSC.panTro4.refGene TxDb.Ptroglodytes.UCSC.panTro5.refGene TxDb.Ptroglodytes.UCSC.panTro6.refGene TxDb.Rnorvegicus.BioMart.igis TxDb.Rnorvegicus.UCSC.rn4.ensGene TxDb.Rnorvegicus.UCSC.rn5.refGene TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq TxDb.Rnorvegicus.UCSC.rn6.refGene TxDb.Rnorvegicus.UCSC.rn7.refGene TxDb.Scerevisiae.UCSC.sacCer2.sgdGene TxDb.Scerevisiae.UCSC.sacCer3.sgdGene TxDb.Sscrofa.UCSC.susScr11.refGene TxDb.Sscrofa.UCSC.susScr3.refGene

MeSHDb (1)

AHMeSHDbs

FRMA (12)

ath1121501frmavecs hgu133a2frmavecs hgu133afrmavecs hgu133plus2frmavecs hthgu133afrmavecs huex.1.0.st.v2frmavecs hugene.1.0.st.v1frmavecs mogene.1.0.st.v1frmavecs mouse4302frmavecs mouse430a2frmavecs rat2302frmavecs ygs98frmavecs

EuPathDB (1)

EuPathDB

ExperimentData (434)

adductData affycompData affydata Affyhgu133A2Expr Affyhgu133aExpr Affyhgu133Plus2Expr AffymetrixDataTestFiles Affymoe4302Expr airway ALL ALLMLL AmpAffyExample antiProfilesData aracne.networks ARRmData AshkenazimSonChr21 ASICSdata AssessORFData AWAggregatorData bcellViper beadarrayExampleData BeadArrayUseCases BeadSorted.Saliva.EPIC beta7 BioImageDbs BioPlex biotmleData biscuiteerData bladderbatch blimaTestingData BloodCancerMultiOmics2017 bodymapRat breakpointRdata breastCancerMAINZ breastCancerNKI breastCancerTRANSBIG breastCancerUNT breastCancerUPP breastCancerVDX brgedata bronchialIL13 bsseqData bugphyzz cancerdata CardinalWorkflows ccdata CCl4 celarefData celldex CellMapperData CENTREprecomputed cfToolsData ChAMPdata ChimpHumanBrainData ChIPDBData chipenrich.data ChIPexoQualExample chipseqDBData ChIPXpressData CLL CLLmethylation CluMSIDdata clustifyrdatahub cMap2data cnvGSAdata COHCAPanno colonCA CONFESSdata ConnectivityMap COPDSexualDimorphism.data CopyhelpeR CopyNeutralIMA CoSIAdata COSMIC.67 CRCL18 crisprScoreData curatedAdipoArray curatedAdipoChIP curatedAdipoRNA curatedBladderData curatedBreastData curatedCRCData curatedMetagenomicData curatedOvarianData curatedPCaData curatedTBData curatedTCGAData CytoMethIC DAPARdata davidTiling depmap derfinderData DeSousa2013 DExMAdata diffloopdata diggitdata DLBCL DMRcatedata DMRsegaldata DNAZooData dominatRData DonaPLLP2013 DoReMiTra dorothea dressCheck DropletTestFiles DrugVsDiseasedata DuoClustering2018 DvDdata dyebiasexamples easierData EatonEtAlChIPseq ecoliLeucine EGSEAdata ELMER.data emtdata EMTscoreData eoPredData EpiMix.data epimutacionsData EpipwR.data estrogen etec16s ewceData faahKO fabiaData FANTOM3and4CAGE ffpeExampleData fibroEset FieldEffectCrc FIs fission Fletcher2013a Fletcher2013b flowPloidyData FlowSorted.Blood.450k FlowSorted.Blood.EPIC FlowSorted.CordBlood.450k FlowSorted.CordBloodCombined.450k FlowSorted.CordBloodNorway.450k FlowSorted.DLPFC.450k flowWorkspaceData fourDNData frmaExampleData furrowSeg gageData gaschYHS gcspikelite gDNAinRNAseqData gDRtestData geneLenDataBase genomationData GenomicDistributionsData GeuvadisTranscriptExpr GIGSEAdata golubEsets gpaExample grndata GSBenchMark GSE103322 GSE13015 GSE159526 GSE62944 GSVAdata GWASdata h5vcData hapmap100khind hapmap100kxba hapmap500knsp hapmap500ksty hapmapsnp5 hapmapsnp6 harbChIP HarmanData HarmonizedTCGAData HCAData HCATonsilData HD2013SGI HDCytoData healthyControlsPresenceChecker healthyFlowData HEEBOdata HelloRangesData hgu133abarcodevecs hgu133plus2barcodevecs hgu133plus2CellScore hgu2beta7 HiBED HiCDataHumanIMR90 HiCDataLymphoblast HiContactsData HighlyReplicatedRNASeq Hiiragi2013 HIVcDNAvantWout03 HMP16SData HMP2Data HSMMSingleCell HumanAffyData humanHippocampus2024 HumanRetinaLRSData humanStemCell IHWpaper Illumina450ProbeVariants.db IlluminaDataTestFiles imcdatasets iModMixData ITALICSData Iyer517 JASPAR2014 JASPAR2016 JohnsonKinaseData KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO kidpack KOdata leeBamViews LegATo leukemiasEset LiebermanAidenHiC2009 ListerEtAlBSseq LRcellTypeMarkers lumiBarnes LungCancerACvsSCCGEO LungCancerLines lungExpression lydata M3DExampleData macrophage MACSdata mammaPrintData maqcExpression4plex MAQCsubset marinerData mCSEAdata mcsurvdata MEDIPSData MEEBOdata MerfishData MetaGxBreast MetaGxOvarian MetaGxPancreas metaMSdata MetaScope MethylAidData methylclockData MethylSeqData MicrobiomeBenchmarkData microbiomeDataSets microRNAome minfiData minfiDataEPIC minionSummaryData miRcompData miRNATarget MMDiffBamSubset MOFAdata mosaicsExample mouse4302barcodevecs MouseAgingData MouseGastrulationData MouseThymusAgeing msd16s msdata msigdb MSMB msPurityData msqc1 mtbls2 MUGAExampleData muleaData multiWGCNAdata muscData muSpaData MutSeqRData mvoutData NanoporeRNASeq nanotubes NCIgraphData NestLink NetActivityData Neve2006 NGScopyData nmrdata nullrangesData NxtIRFdata ObMiTi oct4 octad.db OMICsPCAdata OnassisJavaLibs optimalFlowData orthosData pasilla pasillaBamSubset PasillaTranscriptExpr PathNetData PCHiCdata pd.atdschip.tiling pepDat PepsNMRData PhyloProfileData plotgardenerData prebsdata preciseTADhub PREDAsampledata ProData pRolocdata prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally ProteinGymR ptairData PtH2O2lipids pumadata PWMEnrich.Dmelanogaster.background PWMEnrich.Hsapiens.background PWMEnrich.Mmusculus.background QDNAseq.hg19 QDNAseq.mm10 qPLEXdata QUBICdata raerdata rcellminerData RcisTarget.hg19.motifDBs.cisbpOnly.500bp ReactomeGSA.data RegParallel RforProteomics rheumaticConditionWOLLBOLD RITANdata RMassBankData RNAmodR.Data RNAseqData.HNRNPC.bam.chr14 RnaSeqSampleSizeData RnBeads.hg19 RnBeads.hg38 RnBeads.mm10 RnBeads.mm9 RnBeads.rn5 RRBSdata RTCGA.clinical RTCGA.CNV RTCGA.methylation RTCGA.miRNASeq RTCGA.mRNA RTCGA.mutations RTCGA.PANCAN12 RTCGA.rnaseq RTCGA.RPPA RUVnormalizeData sampleClassifierData SBGNview.data scaeData scanMiRData scATAC.Explorer SCLCBam scMultiome scpdata scRNAseq scTHI.data seq2pathway.data seqc serumStimulation sesameData seventyGeneData SFEData shinyMethylData signatureSearchData SimBenchData simpIntLists Single.mTEC.Transcriptomes SingleCellMultiModal SingleMoleculeFootprintingData smokingMouse SNAData SNAGEEdata SNPhoodData SomatiCAData SomaticCancerAlterations SpatialDatasets spatialDmelxsim spatialLIBD SpikeIn SpikeInSubset spqnData stemHypoxia STexampleData SubcellularSpatialData SVM2CRMdata systemPipeRdata TabulaMurisData TabulaMurisSenisData TargetScoreData TargetSearchData tartare TBX20BamSubset TCGAbiolinksGUI.data TCGAcrcmiRNA TCGAcrcmRNA TCGAMethylation450k TCGAWorkflowData TENET.ExperimentHub TENxBrainData TENxBUSData TENxPBMCData TENxVisiumData TENxXeniumData timecoursedata tinesath1cdf tinesath1probe tissueTreg TMExplorer tofsimsData topdownrdata TransOmicsData tuberculosis TumourMethData tweeDEseqCountData tximportData VariantToolsData VectraPolarisData vulcandata WeberDivechaLCdata WES.1KG.WUGSC WGSmapp xcoredata XhybCasneuf yeastCC yeastExpData yeastGSData yeastNagalakshmi yeastRNASeq zebrafishRNASeq

SpecimenSource (122)

depmap methylclockData

Proteome (12)

AssessORFData AWAggregatorData BioPlex DAPARdata depmap ewceData JohnsonKinaseData pRolocdata ProteinGymR qPLEXdata ReactomeGSA.data scpdata

Genome (67)

Affyhgu133A2Expr Affyhgu133Plus2Expr Affymoe4302Expr aracne.networks AssessORFData bcellViper BeadSorted.Saliva.EPIC BioPlex biscuiteerData breakpointRdata breastCancerVDX bsseqData CCl4 ChIPexoQualExample cnvGSAdata COSMIC.67 CytoMethIC davidTiling depmap DMRcatedata DMRsegaldata dressCheck EpiMix.data ewceData ffpeExampleData fibroEset fission FlowSorted.Blood.EPIC FlowSorted.CordBloodCombined.450k gaschYHS geneLenDataBase genomationData GenomicDistributionsData GeuvadisTranscriptExpr golubEsets GSE103322 GSE159526 GSE62944 hgu133plus2CellScore hgu2beta7 HiBED HiCDataHumanIMR90 leukemiasEset LiebermanAidenHiC2009 LungCancerLines MEDIPSData MMDiffBamSubset MutSeqRData NanoporeRNASeq NxtIRFdata pasilla pasillaBamSubset PasillaTranscriptExpr plotgardenerData preciseTADhub RNAseqData.HNRNPC.bam.chr14 scATAC.Explorer sesameData shinyMethylData SomatiCAData SomaticCancerAlterations TCGAMethylation450k TENET.ExperimentHub tweeDEseqCountData WGSmapp yeastExpData yeastNagalakshmi

StemCell (7)

depmap gageData genomationData MMDiffBamSubset PCHiCdata pRolocdata stemHypoxia

CellCulture (13)

BioImageDbs BioPlex CONFESSdata depmap HD2013SGI HumanRetinaLRSData microRNAome ProteinGymR ptairData PtH2O2lipids scMultiome TENET.ExperimentHub yeastCC

Germline

Somatic (2)

curatedPCaData MutSeqRData

OrganismData (162)

AssessORFData CoSIAdata depmap DExMAdata ELMER.data methylclockData PepsNMRData QDNAseq.hg19 QDNAseq.mm10 QUBICdata TCGAbiolinksGUI.data

Anopheles_gambiae_Data

Apis_mellifera_Data

Arabidopsis_lyrata_Data

Arabidopsis_thaliana_Data (6)

muleaData pd.atdschip.tiling pRolocdata simpIntLists tinesath1cdf tinesath1probe

Bacillus_subtilis_Data (2)

AssessORFData muleaData

Bos_taurus_Data

Caenorhabditis_elegans_Data (2)

CoSIAdata muleaData

Callithrix_jacchus_Data

Canis_familiaris_Data

Ciona_intestinalis_Data

Danio_rerio_Data (3)

CoSIAdata muleaData zebrafishRNASeq

Drosophila_melanogaster_Data (8)

CoSIAdata furrowSeg muleaData pasilla PasillaTranscriptExpr pRolocdata PWMEnrich.Dmelanogaster.background spatialDmelxsim

Drosophila_virilis_Data

Eremothecium_gossypii_Data

Escherichia_coli_Data (4)

AssessORFData muleaData QUBICdata TargetSearchData

Gallus_gallus_Data

Gasterosteus_aculeatus_Data

Glycine_max_Data

Homo_sapiens_Data (121)

Affyhgu133A2Expr Affyhgu133aExpr Affyhgu133Plus2Expr aracne.networks ASICSdata bcellViper beadarrayExampleData BeadSorted.Saliva.EPIC beta7 BioPlex biscuiteerData breakpointRdata breastCancerVDX brgedata ChimpHumanBrainData ChIPDBData ChIPXpressData cMap2data COHCAPanno CONFESSdata CopyNeutralIMA CoSIAdata crisprScoreData curatedMetagenomicData curatedPCaData curatedTBData curatedTCGAData depmap derfinderData DMRcatedata dorothea DrugVsDiseasedata EGSEAdata emtdata eoPredData epimutacionsData fibroEset FieldEffectCrc FIs FlowSorted.Blood.450k FlowSorted.Blood.EPIC FlowSorted.CordBlood.450k FlowSorted.CordBloodCombined.450k FlowSorted.CordBloodNorway.450k FlowSorted.DLPFC.450k frmaExampleData gDNAinRNAseqData GeuvadisTranscriptExpr GIGSEAdata gpaExample GSE103322 GSE159526 GSVAdata HarmanData HD2013SGI HDCytoData hgu133abarcodevecs hgu133plus2barcodevecs hgu133plus2CellScore HiBED HiCDataHumanIMR90 HiCDataLymphoblast HMP16SData HMP2Data HumanAffyData HumanRetinaLRSData humanStemCell Illumina450ProbeVariants.db imcdatasets JohnsonKinaseData KOdata leukemiasEset ListerEtAlBSseq mCSEAdata mcsurvdata MetaGxBreast MetaGxOvarian MetaGxPancreas methylclockData MethylSeqData minfiData minfiDataEPIC miRcompData miRNATarget msigdb muleaData multiWGCNAdata muscData nullrangesData PCHiCdata PepsNMRData plotgardenerData pRolocdata ProteinGymR PWMEnrich.Hsapiens.background QDNAseq.hg19 RcisTarget.hg19.motifDBs.cisbpOnly.500bp ReactomeGSA.data RNAseqData.HNRNPC.bam.chr14 scaeData scanMiRData scMultiome SFEData SpatialDatasets spatialLIBD spqnData stemHypoxia STexampleData SubcellularSpatialData TCGAWorkflowData TENET.ExperimentHub TENxVisiumData tuberculosis TumourMethData tweeDEseqCountData VectraPolarisData vulcandata WeberDivechaLCdata WES.1KG.WUGSC WGSmapp xcoredata

Hordeum_vulgare_Data

Kluyveromyces_lactis_Data

Macaca_mulatta_Data

Magnaporthe_grisea_Data

Medicago_truncatul_Data

Monodelphis_domestica_Data

Neurospora_crassa_Data

Oncorhynchus_mykiss_Data

Oryza_sativa_Data

Pan_paniscus_Data

Pan_troglodytes_Data (2)

ChimpHumanBrainData muleaData

Plasmodium_falciparum_Data

Pseudomonas_aeruginosa_Data (2)

AssessORFData muleaData

Rattus_norvegicus_Data (5)

CCl4 CoSIAdata EGSEAdata muleaData scanMiRData

Saccharomyces_cerevisiae_Data (12)

davidTiling EatonEtAlChIPseq fission gaschYHS harbChIP leeBamViews muleaData yeastCC yeastExpData yeastGSData yeastNagalakshmi yeastRNASeq

Saccharum_officinarum_Data

Schizosaccharomyces_pombe_Data

Staphylococcus_aureus_Data (2)

AssessORFData muleaData

Sus_scrofa_Data

Taeniopygia_guttata_Data

Triticum_aestivum_Data

Vitis_vinifera_Data

Xenopus_laevis_Data

Xenopus_tropicalis_Data

Zea_mays_Data

DiseaseModel (97)

cfToolsData CLLmethylation depmap RegParallel

CancerData (94)

ALL ALLMLL antiProfilesData aracne.networks bcellViper bladderbatch BloodCancerMultiOmics2017 breastCancerMAINZ breastCancerNKI breastCancerTRANSBIG breastCancerUNT breastCancerUPP breastCancerVDX bsseqData cancerdata cfToolsData CLL CLLmethylation colonCA ConnectivityMap COSMIC.67 CRCL18 curatedBladderData curatedBreastData curatedCRCData curatedOvarianData curatedPCaData curatedTCGAData CytoMethIC depmap DeSousa2013 DLBCL easierData EMTscoreData fabiaData Fletcher2013a Fletcher2013b gageData golubEsets GSE103322 GSVAdata h5vcData hapmap100khind hapmap100kxba hapmap500knsp hapmap500ksty hapmapsnp5 HarmonizedTCGAData HD2013SGI Illumina450ProbeVariants.db kidpack KOdata leukemiasEset LungCancerACvsSCCGEO LungCancerLines lungExpression mammaPrintData maqcExpression4plex MetaGxBreast MetaGxOvarian MetaGxPancreas microRNAome Neve2006 NGScopyData octad.db PREDAsampledata ProData prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally rcellminerData RnaSeqSampleSizeData RRBSdata SBGNview.data seventyGeneData shinyMethylData SomatiCAData SomaticCancerAlterations stemHypoxia TCGAcrcmiRNA TCGAcrcmRNA TCGAMethylation450k TCGAWorkflowData TENET.ExperimentHub TMExplorer TumourMethData vulcandata yeastCC

BreastCancerData (18)

breastCancerMAINZ breastCancerNKI breastCancerTRANSBIG breastCancerUNT breastCancerUPP breastCancerVDX curatedBreastData depmap fabiaData Fletcher2013a Fletcher2013b gageData mammaPrintData Neve2006 ProData SBGNview.data seventyGeneData TENET.ExperimentHub

ColonCancerData (8)

antiProfilesData BioPlex bsseqData colonCA depmap DeSousa2013 FieldEffectCrc HD2013SGI

KidneyCancerData (3)

depmap kidpack PREDAsampledata

LeukemiaCancerData (8)

ALL ALLMLL BloodCancerMultiOmics2017 CLL CLLmethylation depmap golubEsets leukemiasEset

LungCancerData (8)

breastCancerVDX depmap LungCancerACvsSCCGEO LungCancerLines lungExpression NGScopyData SCLCBam SubcellularSpatialData

OvarianCancerData (3)

curatedBladderData curatedOvarianData depmap

ProstateCancerData (7)

curatedPCaData depmap prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally

HIVData (1)

HIVcDNAvantWout03

COPDData (1)

COPDSexualDimorphism.data

TechnologyData (310)

ELMER.data gDRtestData imcdatasets MethylAidData OMICsPCAdata TCGAbiolinksGUI.data

FlowCytometryData (5)

flowPloidyData flowWorkspaceData HDCytoData healthyFlowData optimalFlowData

HighThroughputImagingData (3)

CONFESSdata HD2013SGI MerfishData

MassSpectrometryData (26)

ImagingMassSpectrometryData (1)

CardinalWorkflows

qPCRData (4)

curatedBreastData Hiiragi2013 miRcompData seqc

MicrotitrePlateAssayData (1)

HD2013SGI

SAGEData (1)

dyebiasexamples

CGHData (4)

beta7 breastCancerNKI dyebiasexamples PWMEnrich.Hsapiens.background

SequencingData (164)

airway AssessORFData bodymapRat breakpointRdata bsseqData celldex ChIPDBData chipseqDBData clustifyrdatahub CoSIAdata curatedAdipoChIP curatedAdipoRNA diffloopdata DMRcatedata DMRsegaldata DNAZooData DropletTestFiles EatonEtAlChIPseq etec16s ewceData FieldEffectCrc fission fourDNData gDNAinRNAseqData genomationData GeuvadisTranscriptExpr GSVAdata harbChIP HelloRangesData HiContactsData HighlyReplicatedRNASeq HMP16SData HMP2Data humanHippocampus2024 JASPAR2014 leeBamViews LegATo LiebermanAidenHiC2009 ListerEtAlBSseq macrophage marinerData MEDIPSData MetaGxPancreas MetaScope MethylSeqData MicrobiomeBenchmarkData microbiomeDataSets microRNAome minionSummaryData MouseAgingData MouseGastrulationData msd16s MutSeqRData NanoporeRNASeq nanotubes NestLink NGScopyData nullrangesData oct4 octad.db OMICsPCAdata PasillaTranscriptExpr PCHiCdata prebsdata ProteinGymR raerdata RNAmodR.Data RNAseqData.HNRNPC.bam.chr14 RRBSdata sampleClassifierData scATAC.Explorer SCLCBam scMultiome scRNAseq seqc SimBenchData SingleMoleculeFootprintingData SomatiCAData spatialDmelxsim spatialLIBD TBX20BamSubset TENxBrainData TENxBUSData TENxPBMCData tinesath1probe tissueTreg TMExplorer TransOmicsData tuberculosis tximportData VariantToolsData WeberDivechaLCdata WES.1KG.WUGSC WGSmapp yeastNagalakshmi yeastRNASeq

DNASeqData (9)

breakpointRdata GSE103322 GSE62944 LiebermanAidenHiC2009 MMDiffBamSubset muleaData pasillaBamSubset WES.1KG.WUGSC WGSmapp

RNASeqData (78)

airway BioPlex bodymapRat celldex CENTREprecomputed clustifyrdatahub CoSIAdata curatedAdipoRNA curatedOvarianData curatedPCaData derfinderData DoReMiTra DropletTestFiles easierData emtdata EMTscoreData EpiMix.data ewceData FieldEffectCrc fission gDNAinRNAseqData GeuvadisTranscriptExpr GSE103322 GSE62944 HCAData HCATonsilData HighlyReplicatedRNASeq HSMMSingleCell humanHippocampus2024 HumanRetinaLRSData IHWpaper leeBamViews LRcellTypeMarkers LungCancerLines M3DExampleData macrophage microRNAome MouseAgingData MouseGastrulationData multiWGCNAdata NanoporeRNASeq NxtIRFdata ObMiTi oct4 orthosData pasilla pasillaBamSubset PasillaTranscriptExpr prebsdata raerdata ReactomeGSA.data RNAmodR.Data RNAseqData.HNRNPC.bam.chr14 RnaSeqSampleSizeData sampleClassifierData SBGNview.data scRNAseq seqc SimBenchData smokingMouse spatialDmelxsim spqnData TabulaMurisData TabulaMurisSenisData TargetScoreData TBX20BamSubset TENET.ExperimentHub TENxBrainData TENxPBMCData timecoursedata tissueTreg TMExplorer TransOmicsData tweeDEseqCountData tximportData WeberDivechaLCdata yeastRNASeq zebrafishRNASeq

ChIPSeqData (17)

CENTREprecomputed chipseqDBData curatedAdipoChIP dominatRData EatonEtAlChIPseq Fletcher2013b genomationData LiebermanAidenHiC2009 MACSdata MMDiffBamSubset muleaData nullrangesData OMICsPCAdata plotgardenerData TransOmicsData vulcandata yeastNagalakshmi

RIPSeqData

MethylSeqData (2)

MethylSeqData TumourMethData

ExomeSeqData

miRNAData (6)

LiebermanAidenHiC2009 microRNAome muleaData rcellminerData scanMiRData TargetScoreData

SangerSeqData

SmallRNAData (1)

LiebermanAidenHiC2009

MicrobiomeData (10)

bugphyzz curatedMetagenomicData etec16s HMP16SData HMP2Data LegATo MetaScope MicrobiomeBenchmarkData microbiomeDataSets msd16s

SpatialData (13)

HCATonsilData humanHippocampus2024 imcdatasets MerfishData muSpaData SFEData SpatialDatasets spatialLIBD STexampleData SubcellularSpatialData TENxXeniumData VectraPolarisData WeberDivechaLCdata

MicroarrayData (131)

affycompData affydata AffymetrixDataTestFiles ALLMLL AmpAffyExample antiProfilesData beadarrayExampleData BeadArrayUseCases BeadSorted.Saliva.EPIC beta7 bladderbatch blimaTestingData breastCancerMAINZ breastCancerNKI breastCancerTRANSBIG breastCancerUNT breastCancerUPP breastCancerVDX brgedata bronchialIL13 cancerdata ccdata CCl4 CellMapperData ChimpHumanBrainData CLL clustifyrdatahub cMap2data COHCAPanno colonCA ConnectivityMap CopyNeutralIMA curatedAdipoArray curatedBladderData curatedBreastData curatedOvarianData curatedPCaData CytoMethIC davidTiling DeSousa2013 DExMAdata DLBCL DMRcatedata DMRsegaldata DrugVsDiseasedata dyebiasexamples ecoliLeucine epimutacionsData EpipwR.data estrogen ewceData fabiaData ffpeExampleData fibroEset Fletcher2013a FlowSorted.Blood.450k FlowSorted.Blood.EPIC FlowSorted.CordBlood.450k FlowSorted.CordBloodCombined.450k FlowSorted.CordBloodNorway.450k FlowSorted.DLPFC.450k frmaExampleData gageData GSBenchMark GSE13015 GWASdata HarmanData hgu133abarcodevecs hgu133plus2barcodevecs hgu133plus2CellScore HiBED Hiiragi2013 HIVcDNAvantWout03 HumanAffyData IlluminaDataTestFiles KEGGdzPathwaysGEO kidpack leukemiasEset lumiBarnes LungCancerACvsSCCGEO lydata mammaPrintData MAQCsubset mCSEAdata mcsurvdata MetaGxBreast MetaGxOvarian MetaGxPancreas MethylAidData minfiData minfiDataEPIC mouse4302barcodevecs multiWGCNAdata mvoutData pd.atdschip.tiling pepDat PREDAsampledata prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally pumadata rcellminerData rheumaticConditionWOLLBOLD RUVnormalizeData sampleClassifierData SBGNview.data serumStimulation sesameData seventyGeneData SNAGEEdata SpikeIn SpikeInSubset stemHypoxia TCGAWorkflowData TENET.ExperimentHub timecoursedata tinesath1probe tuberculosis XhybCasneuf yeastCC

MultiChannelData (1)

rheumaticConditionWOLLBOLD

OneChannelData (3)

breastCancerNKI breastCancerVDX yeastCC

TwoChannelData (5)

breastCancerUNT CopyNeutralIMA dyebiasexamples HIVcDNAvantWout03 mammaPrintData

GenotypingArrayData

MicroRNAArrayData

mRNAArrayData

ChipOnChipData (11)

breastCancerNKI CENTREprecomputed DLBCL fibroEset genomationData Illumina450ProbeVariants.db leukemiasEset LiebermanAidenHiC2009 lumiBarnes rheumaticConditionWOLLBOLD tinesath1cdf

ReversePhaseProteinArrayData

TissueMicroarrayData (17)

affydata ChimpHumanBrainData colonCA curatedBreastData EpipwR.data ffpeExampleData FlowSorted.Blood.450k FlowSorted.Blood.EPIC FlowSorted.CordBlood.450k FlowSorted.CordBloodCombined.450k FlowSorted.CordBloodNorway.450k FlowSorted.DLPFC.450k leukemiasEset PREDAsampledata rheumaticConditionWOLLBOLD stemHypoxia XhybCasneuf

ProprietaryPlatformsData

AssayDomainData (105)

depmap ELMER.data TCGAbiolinksGUI.data

CopyNumberVariationData (4)

cnvGSAdata curatedPCaData depmap rcellminerData

CpGIslandData (2)

COHCAPanno RRBSdata

SNPData (14)

DMRcatedata DMRsegaldata Fletcher2013b GeuvadisTranscriptExpr gpaExample GWASdata hapmapsnp5 hapmapsnp6 Illumina450ProbeVariants.db leeBamViews pd.atdschip.tiling pumadata rcellminerData VariantToolsData

ExpressionData (87)

BioPlex bodymapRat ccdata celldex CellMapperData clustifyrdatahub CONFESSdata CoSIAdata curatedBladderData curatedBreastData curatedCRCData curatedPCaData DoReMiTra DropletTestFiles emtdata EMTscoreData EpiMix.data ewceData FieldEffectCrc Fletcher2013a gDNAinRNAseqData GeuvadisTranscriptExpr GSE103322 GSVAdata HarmanData HCAData HCATonsilData HDCytoData healthyControlsPresenceChecker hgu133plus2CellScore HighlyReplicatedRNASeq HumanAffyData humanHippocampus2024 HumanRetinaLRSData IHWpaper iModMixData KOdata LRcellTypeMarkers M3DExampleData mammaPrintData MerfishData MetaGxBreast MetaGxOvarian MetaGxPancreas miRcompData MouseAgingData MouseGastrulationData MouseThymusAgeing muleaData multiWGCNAdata muscData muSpaData nanotubes NxtIRFdata octad.db OMICsPCAdata PasillaTranscriptExpr plotgardenerData prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally raerdata rcellminerData ReactomeGSA.data sampleClassifierData scATAC.Explorer scMultiome scpdata scRNAseq SFEData signatureSearchData smokingMouse spatialDmelxsim spatialLIBD spqnData STexampleData TENET.ExperimentHub TENxBrainData TENxBUSData TENxPBMCData TENxVisiumData timecoursedata TMExplorer tuberculosis WeberDivechaLCdata

RepositoryData (95)

depmap healthyControlsPresenceChecker mtbls2 NetActivityData OMICsPCAdata

HapMap (9)

GWASdata hapmap100khind hapmap100kxba hapmap500knsp hapmap500ksty hapmapsnp5 hapmapsnp6 ITALICSData VariantToolsData

GEO (65)

Affyhgu133A2Expr Affyhgu133aExpr Affyhgu133Plus2Expr Affymoe4302Expr airway BioPlex blimaTestingData breastCancerMAINZ breastCancerTRANSBIG breastCancerUNT breastCancerUPP breastCancerVDX ChimpHumanBrainData ChIPXpressData cMap2data COHCAPanno CopyNeutralIMA curatedAdipoArray curatedAdipoChIP curatedAdipoRNA curatedBreastData curatedPCaData curatedTBData DoReMiTra DvDdata EatonEtAlChIPseq eoPredData ffpeExampleData fission gageData GSE103322 GSE159526 healthyControlsPresenceChecker hgu133plus2CellScore HiCDataHumanIMR90 HumanAffyData KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO leukemiasEset LiebermanAidenHiC2009 LungCancerACvsSCCGEO M3DExampleData MAQCsubset mcsurvdata MetaGxBreast MetaGxOvarian MetaGxPancreas muscData ObMiTi PasillaTranscriptExpr prostateCancerCamcap prostateCancerGrasso prostateCancerStockholm prostateCancerTaylor prostateCancerVarambally rheumaticConditionWOLLBOLD RNAseqData.HNRNPC.bam.chr14 SBGNview.data scATAC.Explorer scMultiome SingleCellMultiModal spatialDmelxsim stemHypoxia TMExplorer yeastCC

ArrayExpress (13)

COHCAPanno dyebiasexamples hgu133plus2CellScore HumanAffyData kidpack MetaGxBreast MetaGxOvarian MetaGxPancreas MMDiffBamSubset PREDAsampledata rheumaticConditionWOLLBOLD RNAseqData.HNRNPC.bam.chr14 sampleClassifierData

NCI (9)

LiebermanAidenHiC2009 MetaGxBreast MetaGxOvarian MetaGxPancreas NCIgraphData ProData rcellminerData RNAseqData.HNRNPC.bam.chr14 SomaticCancerAlterations

PathwayInteractionDatabase (2)

FIs PathNetData

Project1000genomes (2)

SomaticCancerAlterations WES.1KG.WUGSC

ENCODE (7)

ChIPDBData genomationData LiebermanAidenHiC2009 nullrangesData OMICsPCAdata plotgardenerData WGSmapp

PackageTypeData (118)

ExperimentHub (113)

adductData AWAggregatorData BeadSorted.Saliva.EPIC BioImageDbs BioPlex biscuiteerData bodymapRat celarefData celldex CENTREprecomputed cfToolsData ChIPDBData chipseqDBData clustifyrdatahub CoSIAdata crisprScoreData curatedAdipoArray curatedAdipoChIP curatedMetagenomicData curatedPCaData curatedTBData curatedTCGAData CytoMethIC depmap DMRcatedata DMRsegaldata DoReMiTra DropletTestFiles easierData emtdata EMTscoreData eoPredData EpiMix.data epimutacionsData EpipwR.data ewceData FieldEffectCrc FlowSorted.CordBloodCombined.450k gDNAinRNAseqData GenomicDistributionsData GSE103322 GSE13015 GSE159526 HCAData HCATonsilData HDCytoData HiContactsData HighlyReplicatedRNASeq HMP16SData humanHippocampus2024 imcdatasets iModMixData JohnsonKinaseData LRcellTypeMarkers MACSdata marinerData MerfishData MetaGxBreast MetaGxOvarian MetaGxPancreas methylclockData MethylSeqData microbiomeDataSets MouseAgingData MouseGastrulationData MouseThymusAgeing msigdb muleaData multiWGCNAdata muscData muSpaData MutSeqRData NanoporeRNASeq NestLink nmrdata nullrangesData NxtIRFdata ObMiTi octad.db orthosData PhyloProfileData preciseTADhub ProteinGymR raerdata scaeData scMultiome scpdata scRNAseq sesameData SFEData signatureSearchData SimBenchData SingleCellMultiModal SingleMoleculeFootprintingData smokingMouse SpatialDatasets spatialDmelxsim spatialLIBD STexampleData SubcellularSpatialData TabulaMurisSenisData tartare TENET.ExperimentHub TENxBUSData TENxPBMCData TENxVisiumData TENxXeniumData TransOmicsData tuberculosis TumourMethData VectraPolarisData WeberDivechaLCdata xcoredata

ImmunoOncologyData (5)

easierData HDCytoData imcdatasets muscData optimalFlowData

Workflow (25)

BasicWorkflow (5)

arrays fluentGenomics liftOver seqpac sequencing

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annotation CAGEWorkflow seqpac variants

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BP4RNAseq CAGEWorkflow EGSEA123 ExpHunterSuite ExpressionNormalizationWorkflow fluentGenomics GeoMxWorkflows RNAseq123 rnaseqDTU rnaseqGene RnaSeqGeneEdgeRQL seqpac

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chipseqDB csawUsersGuide generegulation methylationArrayAnalysis seqpac

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highthroughputassays

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chipseqDB cytofWorkflow EGSEA123 ExpressionNormalizationWorkflow GeoMxWorkflows highthroughputassays RNAseq123 rnaseqDTU rnaseqGene RnaSeqGeneEdgeRQL sequencing simpleSingleCell variants