[ { "data": "Software (1975)", "attr": { "packageList": "a4,a4Base,a4Classif,a4Core,a4Preproc,a4Reporting,ABAEnrichment,ABarray,abseqR,ABSSeq,acde,ACE,aCGH,ACME,ADaCGH2,ADAM,ADAMgui,adaptest,adductomicsR,ADImpute,adSplit,AffiXcan,affxparser,affy,affycomp,AffyCompatible,affyContam,affycoretools,AffyExpress,affyILM,affyio,affylmGUI,affyPara,affyPLM,affyQCReport,AffyRNADegradation,AGDEX,aggregateBioVar,agilp,AgiMicroRna,AIMS,ALDEx2,alevinQC,AllelicImbalance,AlphaBeta,alpine,ALPS,AlpsNMR,alsace,altcdfenvs,AMARETTO,AMOUNTAIN,amplican,Anaquin,ANCOMBC,AneuFinder,ANF,animalcules,annaffy,annmap,annotate,AnnotationDbi,AnnotationFilter,AnnotationForge,AnnotationFuncs,AnnotationHub,AnnotationHubData,annotationTools,annotatr,anota,anota2seq,antiProfiles,AnVIL,AnVILBilling,AnVILPublish,APAlyzer,apComplex,apeglm,appreci8R,aroma.light,ArrayExpress,ArrayExpressHTS,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,ArrayTV,ARRmNormalization,artMS,ASAFE,ASEB,ASGSCA,ASICS,ASpediaFI,ASpli,AssessORF,ASSET,ASSIGN,ATACseqQC,atSNP,attract,AUCell,Autotuner,AWFisher,BaalChIP,BAC,bacon,BADER,BadRegionFinder,BAGS,ballgown,bambu,bamsignals,BANDITS,banocc,basecallQC,BaseSpaceR,Basic4Cseq,BASiCS,BasicSTARRseq,basilisk,basilisk.utils,batchelor,BatchQC,BayesKnockdown,BayesSpace,bayNorm,baySeq,BBCAnalyzer,BCRANK,bcSeq,BDMMAcorrect,beachmat,beadarray,beadarraySNP,BeadDataPackR,BEARscc,BEAT,BEclear,BgeeCall,BgeeDB,BGmix,bgx,BHC,BicARE,BiFET,BiGGR,bigmelon,bigmemoryExtras,bigPint,bioassayR,Biobase,biobroom,biobtreeR,bioCancer,BiocCaseStudies,BiocCheck,BiocDockerManager,BiocFileCache,BiocGenerics,biocGraph,BiocIO,BiocNeighbors,BiocOncoTK,BioCor,BiocParallel,BiocPkgTools,BiocSet,BiocSingular,BiocSklearn,BiocStyle,biocthis,BiocVersion,biocViews,BiocWorkflowTools,bioDist,biomaRt,biomformat,BioMM,BioMVCClass,biomvRCNS,BioNet,BioNetStat,BioQC,BioSeqClass,biosigner,Biostrings,BioTIP,biotmle,biovizBase,BiRewire,biscuiteer,BiSeq,BitSeq,blacksheepr,blima,BLMA,bluster,bnbc,BPRMeth,BRAIN,brainflowprobes,BrainSABER,BrainStars,branchpointer,breakpointR,brendaDb,BRGenomics,bridge,BridgeDbR,BrowserViz,BSgenome,bsseq,BubbleTree,BufferedMatrix,BufferedMatrixMethods,BUMHMM,bumphunter,BUS,BUScorrect,BUSpaRse,CAFE,CAGEfightR,CAGEr,calm,CAMERA,canceR,cancerclass,CancerInSilico,CancerMutationAnalysis,CancerSubtypes,CAnD,caOmicsV,Cardinal,CARNIVAL,casper,CATALYST,Category,categoryCompare,CausalR,cbaf,cBioPortalData,ccfindR,ccmap,CCPROMISE,ccrepe,celaref,celda,CellaRepertorium,cellbaseR,CellBench,cellHTS2,cellity,CellMapper,CellMixS,CellNOptR,cellscape,CellScore,CellTrails,cellTree,CEMiTool,ceRNAnetsim,CeTF,CexoR,CFAssay,cfDNAPro,CGEN,CGHbase,CGHcall,cghMCR,CGHnormaliter,CGHregions,ChAMP,CHARGE,ChemmineOB,ChemmineR,CHETAH,ChIC,Chicago,chimera,chimeraviz,ChIPanalyser,ChIPComp,chipenrich,ChIPexoQual,ChIPpeakAnno,ChIPQC,ChIPseeker,chipseq,ChIPseqR,ChIPSeqSpike,ChIPsim,ChIPXpress,chopsticks,chromDraw,ChromHeatMap,chromPlot,ChromSCape,chromstaR,chromswitch,chromVAR,CHRONOS,cicero,CINdex,circRNAprofiler,cisPath,CiteFuse,ClassifyR,cleanUpdTSeq,cleaver,clippda,clipper,cliqueMS,Clomial,Clonality,clonotypeR,clst,clstutils,CluMSID,clustComp,clusterExperiment,ClusterJudge,clusterProfiler,clusterSeq,ClusterSignificance,clusterStab,clustifyr,CMA,cmapR,cn.farms,cn.mops,CNAnorm,CNEr,CNORdt,CNORfeeder,CNORfuzzy,CNORode,CNTools,CNVfilteR,cnvGSA,CNVPanelizer,CNVRanger,CNVrd2,CNVtools,CoCiteStats,COCOA,codelink,CODEX,coexnet,CoGAPS,cogena,coGPS,COHCAP,cola,combi,coMET,compartmap,COMPASS,compcodeR,compEpiTools,CompGO,ComplexHeatmap,CONFESS,consensus,ConsensusClusterPlus,consensusDE,consensusOV,consensusSeekeR,contiBAIT,conumee,convert,copa,copynumber,CopyNumberPlots,CopywriteR,coRdon,CoRegFlux,CoRegNet,CoreGx,Cormotif,CorMut,corral,CORREP,coseq,cosmiq,COSNet,CountClust,countsimQC,covEB,CoverageView,covRNA,cpvSNP,cqn,CRImage,CRISPRseek,crisprseekplus,CrispRVariants,crlmm,CrossICC,crossmeta,CSAR,csaw,CSSP,CSSQ,ctc,ctgGEM,cTRAP,ctsGE,cummeRbund,customCMPdb,customProDB,cycle,cydar,CytoDx,cytofast,cytolib,cytomapper,CytoML,CytoTree,dada2,dagLogo,daMA,DAMEfinder,DaMiRseq,DAPAR,DART,dasper,DBChIP,dcanr,dcGSA,ddCt,ddPCRclust,dearseq,debCAM,debrowser,DECIPHER,deco,DEComplexDisease,decompTumor2Sig,DeconRNASeq,decontam,DeepBlueR,deepSNV,DEFormats,DegNorm,DEGraph,DEGreport,DEGseq,DelayedArray,DelayedDataFrame,DelayedMatrixStats,deltaCaptureC,deltaGseg,DeMAND,DeMixT,densvis,DEP,DepecheR,DEqMS,derfinder,derfinderHelper,derfinderPlot,DEScan2,DESeq,DESeq2,DEsingle,destiny,DEsubs,DEWSeq,DEXSeq,dexus,DFP,DIAlignR,DiffBind,diffcoexp,diffcyt,diffGeneAnalysis,diffHic,DiffLogo,diffloop,diffuStats,diggit,Director,DirichletMultinomial,discordant,DiscoRhythm,distinct,dittoSeq,divergence,dks,DMCFB,DMCHMM,DMRcaller,DMRcate,DMRforPairs,DMRScan,dmrseq,DNABarcodeCompatibility,DNABarcodes,DNAcopy,DNAshapeR,DominoEffect,doppelgangR,Doscheda,DOSE,doseR,dpeak,drawProteins,DRIMSeq,DriverNet,DropletUtils,DrugVsDisease,DSS,DTA,dualKS,Dune,dupRadar,dyebias,DynDoc,EasyqpcR,easyreporting,easyRNASeq,EBarrays,EBcoexpress,EBImage,EBSEA,EBSeq,EBSeqHMM,ecolitk,EDASeq,EDDA,edge,edgeR,eegc,EGAD,EGSEA,eiR,eisa,eisaR,ELBOW,ELMER,EMDomics,EmpiricalBrownsMethod,ENCODExplorer,EnhancedVolcano,EnMCB,ENmix,EnrichedHeatmap,EnrichmentBrowser,enrichplot,enrichTF,ensembldb,ensemblVEP,ENVISIONQuery,EpiDISH,epigenomix,epihet,epiNEM,EpiTxDb,epivizr,epivizrChart,epivizrData,epivizrServer,epivizrStandalone,erccdashboard,erma,ERSSA,esATAC,escape,esetVis,eudysbiome,evaluomeR,EventPointer,ExCluster,ExiMiR,exomeCopy,exomePeak2,ExperimentHub,ExperimentHubData,ExperimentSubset,explorase,ExploreModelMatrix,ExpressionAtlas,ExpressionView,fabia,factDesign,FamAgg,famat,farms,fastLiquidAssociation,FastqCleaner,fastseg,FCBF,fCCAC,fCI,fcoex,fcScan,fdrame,FELLA,ffpe,FGNet,fgsea,FilterFFPE,FindMyFriends,FISHalyseR,fishpond,FitHiC,flagme,flowAI,flowBeads,flowBin,flowcatchR,flowCHIC,flowCL,flowClean,flowClust,flowCore,flowCut,flowCyBar,flowDensity,flowFit,flowFP,flowMap,flowMatch,flowMeans,flowMerge,flowPeaks,flowPloidy,flowPlots,FlowRepositoryR,FlowSOM,flowSpecs,flowSpy,flowStats,flowTime,flowTrans,flowType,flowUtils,flowViz,flowVS,flowWorkspace,fmcsR,fmrs,focalCall,FoldGO,FourCSeq,FRASER,frenchFISH,FRGEpistasis,frma,frmaTools,FScanR,FunChIP,FunciSNP,funtooNorm,GA4GHclient,GA4GHshiny,gaga,gage,gaggle,gaia,GAPGOM,GAprediction,garfield,GARS,GateFinder,gcapc,gcatest,gCrisprTools,gcrma,GCSConnection,GCSFilesystem,GCSscore,GDCRNATools,GDSArray,gdsfmt,GEM,gemini,genArise,genbankr,GeneAccord,GeneAnswers,geneAttribution,GeneBreak,geneClassifiers,GeneExpressionSignature,genefilter,genefu,GeneGA,GeneGeneInteR,GeneMeta,GeneNetworkBuilder,GeneOverlap,geneplast,geneplotter,geneRecommender,GeneRegionScan,geneRxCluster,GeneSelectMMD,GENESIS,GeneStructureTools,geNetClassifier,GeneticsDesign,GeneticsPed,GeneTonic,geneXtendeR,GENIE3,genoCN,GenoGAM,genomation,GenomeInfoDb,genomeIntervals,genomes,GenomicAlignments,GenomicDataCommons,GenomicFeatures,GenomicFiles,GenomicInteractions,GenomicOZone,GenomicRanges,GenomicScores,GenomicTuples,genoset,genotypeeval,genphen,GenRank,GenVisR,GEOmetadb,GEOquery,GEOsubmission,gep2pep,gespeR,getDEE2,GEWIST,GGBase,ggbio,ggcyto,GGPA,GGtools,ggtree,ggtreeExtra,GIGSEA,girafe,GISPA,GLAD,GladiaTOX,Glimma,glmGamPoi,glmSparseNet,GlobalAncova,globalSeq,globaltest,gmapR,GmicR,gmoviz,GMRP,GNET2,GOexpress,GOfuncR,GOFunction,GOpro,goProfiles,GOSemSim,goseq,GOSim,goSTAG,GOstats,GOsummaries,GOTHiC,goTools,GPA,gpart,gpls,gprege,gpuMagic,gQTLBase,gQTLstats,gramm4R,graper,graph,GraphAlignment,GraphAT,graphite,GraphPAC,GRENITS,GreyListChIP,GRmetrics,groHMM,GRridge,GSALightning,GSAR,GSCA,gscreend,GSEABase,GSEABenchmarkeR,GSEAlm,GSEAmining,gsean,GSgalgoR,GSReg,GSRI,GSVA,gtrellis,GUIDEseq,Guitar,Gviz,GWAS.BAYES,gwascat,GWASTools,gwasurvivr,GWENA,h5vc,hapFabia,Harman,Harshlight,HCABrowser,HCAExplorer,HCAMatrixBrowser,HDF5Array,HDTD,heatmaps,Heatplus,HelloRanges,HELP,HEM,Herper,hiAnnotator,HIBAG,HiCBricks,HiCcompare,hicrep,hierGWAS,hierinf,HilbertCurve,HilbertVis,HilbertVisGUI,HiLDA,hipathia,HIPPO,hiReadsProcessor,HIREewas,HiTC,hmdbQuery,HMMcopy,hopach,HPAanalyze,hpar,HPAStainR,HTqPCR,HTSeqGenie,HTSFilter,HumanTranscriptomeCompendium,hummingbird,HybridMTest,hypeR,hyperdraw,hypergraph,iASeq,iasva,iBBiG,ibh,iBMQ,iCARE,Icens,icetea,iCheck,iChip,iClusterPlus,iCNV,iCOBRA,ideal,IdeoViz,idiogram,idpr,idr2d,iGC,IgGeneUsage,igvR,IHW,illuminaio,ILoReg,imageHTS,IMAS,Imetagene,IMMAN,ImmuneSpaceR,immunoClust,IMPCdata,ImpulseDE,ImpulseDE2,impute,INDEED,infercnv,infinityFlow,Informeasure,InPAS,INPower,INSPEcT,InTAD,intansv,InteractionSet,interactiveDisplay,interactiveDisplayBase,IntEREst,InterMineR,IntramiRExploreR,inveRsion,IONiseR,iPAC,ipdDb,IPO,IRanges,ISAnalytics,iSEE,iSEEu,iSeq,isobar,IsoCorrectoR,IsoCorrectoRGUI,IsoformSwitchAnalyzeR,IsoGeneGUI,ISoLDE,isomiRs,ITALICS,iterativeBMA,iterativeBMAsurv,iterClust,iteremoval,IVAS,ivygapSE,IWTomics,joda,JunctionSeq,karyoploteR,KCsmart,kebabs,KEGGgraph,KEGGlincs,keggorthology,KEGGprofile,KEGGREST,KinSwingR,kissDE,KnowSeq,LACE,lapmix,LBE,ldblock,LEA,LedPred,lefser,les,levi,lfa,limma,limmaGUI,LINC,LineagePulse,LinkHD,Linnorm,lionessR,lipidr,LiquidAssociation,lmdme,LOBSTAHS,loci2path,logicFS,logitT,Logolas,LOLA,LoomExperiment,LowMACA,LPE,LPEadj,lpNet,lpsymphony,LRBaseDbi,lumi,LymphoSeq,M3C,M3Drop,maanova,Maaslin2,macat,maCorrPlot,MACPET,MACSQuantifyR,made4,MADSEQ,maftools,MAGeCKFlute,maigesPack,MAIT,makecdfenv,MANOR,MantelCorr,mAPKL,maPredictDSC,mapscape,marr,marray,martini,maser,maSigPro,maskBAD,MassArray,massiR,MassSpecWavelet,MAST,matchBox,MatrixGenerics,MatrixRider,matter,MBAmethyl,MBASED,MBCB,mbkmeans,mBPCR,MBQN,MBttest,mcaGUI,MCbiclust,mCSEA,mdgsa,mdp,mdqc,MDTS,MEAL,MeasurementError.cor,MEAT,MEB,MEDIPS,MEDME,megadepth,MEIGOR,Melissa,Mergeomics,MeSHDbi,meshes,meshr,MesKit,messina,metaArray,Metab,metabCombiner,metabolomicsWorkbenchR,metabomxtr,MetaboSignal,metaCCA,MetaCyto,metagene,metagene2,metagenomeFeatures,metagenomeSeq,metahdep,metaMS,MetaNeighbor,metaSeq,metaseqR,metaseqR2,metavizr,MetaVolcanoR,MetCirc,MethCP,methimpute,methInheritSim,MethPed,MethReg,methrix,MethTargetedNGS,methVisual,methyAnalysis,MethylAid,methylCC,methylGSA,methylInheritance,methylKit,MethylMix,methylMnM,methylPipe,MethylSeekR,methylSig,methylumi,methyvim,MetID,MetNet,mfa,Mfuzz,MGFM,MGFR,mgsa,MiChip,microbiome,microbiomeDASim,microbiomeExplorer,MicrobiotaProcess,microRNA,MIGSA,mimager,MIMOSA,MineICA,minet,minfi,MinimumDistance,MiPP,MIRA,MiRaGE,miRBaseConverter,miRcomp,mirIntegrator,miRLAB,miRmine,miRNAmeConverter,miRNApath,miRNAtap,miRSM,miRspongeR,Mirsynergy,missMethyl,missRows,mitch,mixOmics,MLInterfaces,MLP,MLSeq,MMAPPR2,MMDiff2,MmPalateMiRNA,MMUPHin,mnem,MODA,Modstrings,MOFA,MOFA2,MOGAMUN,mogsa,MOMA,monocle,MoonlightR,mosaics,MOSim,motifbreakR,motifcounter,MotifDb,motifmatchr,motifStack,MotIV,MouseFM,MPFE,mpra,MPRAnalyze,msa,MsCoreUtils,MSEADbi,msgbsR,MSGFgui,MSGFplus,msImpute,msmsEDA,msmsTests,MSnbase,MSnID,MSPrep,msPurity,MSstats,MSstatsConvert,MSstatsPTM,MSstatsQC,MSstatsQCgui,MSstatsSampleSize,MSstatsTMT,MSstatsTMTPTM,Mulcom,MultiAssayExperiment,MultiBaC,multiClust,multicrispr,MultiDataSet,multiGSEA,multiHiCcompare,MultiMed,multiMiR,multiOmicsViz,multiscan,multtest,muscat,muscle,musicatk,MutationalPatterns,MVCClass,MWASTools,mygene,myvariant,mzID,mzR,NADfinder,NanoMethViz,NanoStringDiff,NanoStringQCPro,nanotatoR,NarrowPeaks,NBAMSeq,NBSplice,ncdfFlow,ncGTW,NCIgraph,ncRNAtools,ndexr,nearBynding,Nebulosa,NeighborNet,netbenchmark,netbiov,netboost,netboxr,netDx,nethet,NetPathMiner,netprioR,netReg,netresponse,NetSAM,netSmooth,networkBMA,NewWave,ngsReports,nnNorm,NOISeq,nondetects,NoRCE,normalize450K,NormalyzerDE,NormqPCR,normr,NPARC,npGSEA,NTW,nucleoSim,nucleR,nuCpos,NuPoP,occugene,OCplus,odseq,OGSA,oligo,oligoClasses,OLIN,OLINgui,OmaDB,omicade4,OmicCircos,omicplotR,omicRexposome,OmicsLonDA,OmicsMarkeR,OMICsPCA,omicsPrint,Omixer,OmnipathR,Onassis,oncomix,OncoScore,OncoSimulR,oneSENSE,onlineFDR,ontoProc,openCyto,openPrimeR,openPrimeRui,OpenStats,oposSOM,oppar,oppti,optimalFlow,OPWeight,OrderedList,ORFik,Organism.dplyr,OrganismDbi,OSAT,Oscope,OTUbase,OutlierD,OUTRIDER,OVESEG,PAA,packFinder,padma,PADOG,pageRank,PAIRADISE,paircompviz,pandaR,panelcn.mops,panp,PANR,PanVizGenerator,parglms,parody,PAST,Path2PPI,pathifier,PathNet,PathoStat,pathprint,pathRender,pathVar,pathview,pathwayPCA,PathwaySplice,paxtoolsr,pcaExplorer,pcaMethods,PCAN,PCAtools,pcot2,PCpheno,pcxn,pdInfoBuilder,PeacoQC,peakPantheR,PECA,peco,PepsNMR,pepStat,pepXMLTab,PERFect,periodicDNA,perturbatr,PGA,pgca,PGSEA,phantasus,PharmacoGx,phemd,phenopath,phenoTest,PhenStat,philr,phosphonormalizer,PhosR,PhyloProfile,phyloseq,Pi,piano,pickgene,PICS,Pigengene,PING,pipeComp,pipeFrame,pkgDepTools,plethy,plgem,plier,PloGO2,plotGrouper,PLPE,plrs,plyranges,pmm,pmp,podkat,pogos,polyester,Polyfit,POMA,POST,PoTRA,powerTCR,PPInfer,ppiStats,pqsfinder,prada,pram,prebs,preciseTAD,PrecisionTrialDrawer,PREDA,predictionet,preprocessCore,primirTSS,PrInCE,Prize,proActiv,proBAMr,proBatch,PROcess,procoil,proDA,proFIA,profileplyr,profileScoreDist,progeny,projectR,pRoloc,pRolocGUI,PROMISE,PROPER,PROPS,Prostar,proteinProfiles,ProteomicsAnnotationHubData,ProteoMM,ProtGenerics,PSEA,psichomics,PSICQUIC,psygenet2r,PubScore,pulsedSilac,puma,PureCN,pvac,pvca,Pviz,PWMEnrich,pwOmics,pwrEWAS,qckitfastq,qcmetrics,QDNAseq,QFeatures,qpcrNorm,qpgraph,qPLEXanalyzer,qrqc,qsea,qsmooth,QSutils,Qtlizer,quantro,quantsmooth,QuartPAC,QuasR,QuaternaryProd,QUBIC,qusage,qvalue,R3CPET,r3Cseq,R453Plus1Toolbox,R4RNA,RadioGx,RaggedExperiment,rain,rama,ramwas,RandomWalkRestartMH,randPack,randRotation,RankProd,RareVariantVis,Rariant,RbcBook1,RBGL,RBioinf,rBiopaxParser,RBM,Rbowtie,Rbowtie2,rbsurv,Rcade,RCAS,RCASPAR,rcellminer,rCGH,RchyOptimyx,RcisTarget,RCM,Rcpi,Rcwl,RcwlPipelines,RCy3,RCyjs,RDAVIDWebService,rDGIdb,Rdisop,RDRToolbox,ReactomeGSA,ReactomePA,ReadqPCR,reb,REBET,rebook,receptLoss,reconsi,recount,recount3,recountmethylation,recoup,RedeR,REDseq,RefPlus,RegEnrich,regioneR,regionReport,regsplice,regutools,REMP,Repitools,ReportingTools,RepViz,ReQON,ResidualMatrix,restfulSE,rexposome,rfaRm,Rfastp,rfPred,rGADEM,RGalaxy,Rgin,RGMQL,RGraph2js,Rgraphviz,rGREAT,RGSEA,rgsepd,rhdf5,rhdf5client,rhdf5filters,Rhdf5lib,Rhisat2,Rhtslib,RiboProfiling,ribor,riboSeqR,ribosomeProfilingQC,RImmPort,Ringo,RIPAT,Risa,RITAN,RIVER,RJMCMCNucleosomes,RLMM,Rmagpie,RMassBank,rmelting,RmiR,Rmmquant,RNAAgeCalc,RNAdecay,rnaEditr,RNAinteract,RNAither,RNAmodR,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,RNAprobR,RNAsense,rnaseqcomp,rnaSeqMap,RNASeqPower,RNASeqR,RnaSeqSampleSize,RnBeads,Rnits,roar,ROC,ROCpAI,Roleswitch,rols,ROntoTools,ropls,ROSeq,ROTS,RPA,RProtoBufLib,RpsiXML,rpx,Rqc,rqt,rqubic,rRDP,RRHO,rrvgo,Rsamtools,rsbml,rScudo,rsemmed,RSeqAn,Rsubread,RSVSim,rSWeeP,rTANDEM,RTCA,RTCGA,RTCGAToolbox,RTN,RTNduals,RTNsurvival,RTopper,Rtpca,rtracklayer,Rtreemix,rTRM,rTRMui,runibic,RUVcorr,RUVnormalize,RUVSeq,RVS,rWikiPathways,S4Vectors,safe,sagenhaft,SAGx,SAIGEgds,samExploreR,sampleClassifier,SamSPECTRAL,sangeranalyseR,sangerseqR,sapFinder,sarks,savR,SBGNview,SBMLR,SC3,Scale4C,scAlign,SCAN.UPC,SCANVIS,SCATE,scater,scBFA,SCBN,scCB2,scClassify,scDataviz,scDblFinder,scDD,scde,scds,SCFA,scFeatureFilter,scGPS,schex,scHOT,ScISI,scMAGeCK,scmap,scMerge,scmeth,SCnorm,scone,Sconify,SCOPE,scoreInvHap,scp,scPCA,scPipe,scran,scRecover,scRepertoire,scruff,scry,scsR,scTensor,scTGIF,scTHI,scuttle,SDAMS,segmentSeq,selectKSigs,SELEX,SemDist,semisup,SEPIRA,seq2pathway,SeqArray,seqbias,seqCAT,seqCNA,seqcombo,SeqGate,SeqGSEA,seqLogo,seqPattern,seqplots,seqsetvis,SeqSQC,seqTools,SeqVarTools,sesame,SEtools,sevenbridges,sevenC,SGSeq,SharedObject,shinyMethyl,shinyTANDEM,ShortRead,SIAMCAT,SICtools,sigaR,SigCheck,sigFeature,SigFuge,siggenes,sights,signatureSearch,signeR,signet,sigPathway,SigsPack,sigsquared,SIM,SIMAT,SimBindProfiles,SIMD,SimFFPE,similaRpeak,SIMLR,simpleaffy,simplifyEnrichment,simulatorZ,sincell,SingleCellExperiment,SingleCellSignalR,singleCellTK,SingleR,singscore,SISPA,sitePath,sizepower,skewr,slalom,SLGI,slingshot,slinky,SLqPCR,SMAD,SMAP,SMITE,SNAGEE,snapCGH,snapcount,snifter,snm,SNPediaR,SNPhood,SNPRelate,snpStats,soGGi,sojourner,SomaticSignatures,SpacePAC,Spaniel,sparseDOSSA,sparseMatrixStats,sparsenetgls,SparseSignatures,SpatialCPie,SpatialDecon,SpatialExperiment,spatialHeatmap,specL,SpeCond,Spectra,SpectralTAD,SPEM,SPIA,spicyR,SpidermiR,spikeLI,spkTools,splatter,SplicingGraphs,splineTimeR,SPLINTER,splots,SPONGE,spotSegmentation,spqn,SPsimSeq,SQLDataFrame,SQUADD,sRACIPE,SRAdb,SRGnet,srnadiff,sscore,sscu,sSeq,ssize,SSPA,ssPATHS,ssrch,ssviz,stageR,STAN,staRank,StarBioTrek,Starr,STATegRa,statTarget,stepNorm,strandCheckR,Streamer,STRINGdb,STROMA4,struct,Structstrings,structToolbox,StructuralVariantAnnotation,SubCellBarCode,subSeq,SummarizedBenchmark,SummarizedExperiment,supraHex,survcomp,survtype,Sushi,sva,SVAPLSseq,SWATH2stats,SwathXtend,swfdr,SwimR,switchBox,switchde,synapter,synergyfinder,SynExtend,synlet,SynMut,systemPipeR,systemPipeShiny,TADCompare,TAPseq,target,TargetScore,TargetSearch,TarSeqQC,TBSignatureProfiler,TCC,TCGAbiolinks,TCGAbiolinksGUI,TCGAutils,TCseq,TDARACNE,tenXplore,TEQC,ternarynet,TFARM,TFBSTools,TFEA.ChIP,TFHAZ,TFutils,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,tigre,TileDBArray,tilingArray,timecourse,timeOmics,timescape,TimeSeriesExperiment,TimiRGeN,TIN,TissueEnrich,TitanCNA,tkWidgets,TMixClust,TNBC.CMS,TnT,TOAST,tofsims,tomoda,ToPASeq,topconfects,topdownr,topGO,ToxicoGx,TPP,TPP2D,tracktables,trackViewer,tradeSeq,transcriptogramer,transcriptR,transite,tRanslatome,transomics2cytoscape,TransView,traseR,TreeAndLeaf,treeio,TreeSummarizedExperiment,trena,Trendy,trigger,trio,triplex,tRNA,tRNAdbImport,tRNAscanImport,TRONCO,TSCAN,tscR,tspair,TSRchitect,TTMap,TurboNorm,TVTB,tweeDEseq,twilight,twoddpcr,tximeta,tximport,TxRegInfra,TypeInfo,Ularcirc,UMI4Cats,uncoverappLib,UNDO,unifiedWMWqPCR,UniProt.ws,Uniquorn,universalmotif,uSORT,VanillaICE,variancePartition,VariantAnnotation,VariantExperiment,VariantFiltering,VariantTools,vasp,VaSP,vbmp,VCFArray,VegaMC,velociraptor,VennDetail,VERSO,vidger,viper,ViSEAGO,VplotR,vsn,vtpnet,vulcan,waddR,wateRmelon,wavClusteR,weaver,webbioc,weitrix,widgetTools,wiggleplotr,wpm,Wrench,XBSeq,XCIR,xcms,XDE,Xeva,XINA,xmapbridge,xps,XVector,yamss,YAPSA,yaqcaffy,yarn,zellkonverter,zFPKM,zinbwave,zlibbioc", "id": "Software" }, "children": [ { "data": "AssayDomain (790)", "attr": { "packageList": "cbaf,GWAS.BAYES,iGC,MetID,nondetects,pgca,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment", "id": "AssayDomain" }, "children": [ { "data": "aCGH (13)", "attr": { "packageList": "biomvRCNS,CINdex,Clonality,copynumber,gaia,GeneBreak,KCsmart,mBPCR,RCASPAR,rcellminer,rCGH,sigaR,VegaMC", "id": "aCGH" }, "children": [ ] }, { "data": "CellBasedAssays (62)", "attr": { "packageList": "bioassayR,cellHTS2,CellNOptR,CFAssay,ChemmineOB,ChemmineR,cicero,CNORdt,CNORfeeder,CNORode,contiBAIT,CytoDx,CytoTree,DepecheR,destiny,diffcyt,eiR,flowBeads,flowBin,flowCHIC,flowCore,flowCut,flowCyBar,flowFit,flowFP,flowPlots,FlowSOM,flowSpecs,flowSpy,flowStats,flowTime,flowUtils,flowViz,flowVS,fmcsR,gespeR,ggcyto,GRmetrics,imageHTS,immunoClust,ImpulseDE2,infinityFlow,iSEE,iSEEu,LineagePulse,MetaCyto,MIMOSA,MPRAnalyze,netprioR,PANR,perturbatr,prada,rcellminer,RNAinteract,RNAither,RTCA,scp,sights,spatialHeatmap,spicyR,staRank,synlet", "id": "CellBasedAssays" }, "children": [ ] }, { "data": "ChIPchip (9)", "attr": { "packageList": "ChIPpeakAnno,ChIPXpress,iChip,les,motifStack,MotIV,rGADEM,sevenC,Starr", "id": "ChIPchip" }, "children": [ ] }, { "data": "CopyNumberVariation (68)", "attr": { "packageList": "ACE,aCGH,AMARETTO,AneuFinder,ArrayTV,beadarraySNP,BiocOncoTK,biomvRCNS,BubbleTree,CGHbase,cghMCR,CGHregions,CINdex,cn.farms,cn.mops,CNAnorm,CNTools,CNVfilteR,CNVPanelizer,CNVRanger,CNVrd2,CODEX,conumee,copynumber,CopyNumberPlots,CopywriteR,crlmm,DNAcopy,exomeCopy,fastseg,gaia,GeneBreak,GenomicOZone,genoset,GenRank,GLAD,HMMcopy,iCNV,iGC,infercnv,ITALICS,karyoploteR,KCsmart,MADSEQ,MANOR,mBPCR,MEDIPS,MinimumDistance,OGSA,panelcn.mops,pathwayPCA,PREDA,PureCN,QDNAseq,qsea,quantsmooth,rcellminer,rCGH,reb,regioneR,SCOPE,seqCNA,SMAP,snapCGH,sparsenetgls,TitanCNA,VanillaICE,VegaMC", "id": "CopyNumberVariation" }, "children": [ ] }, { "data": "CpGIsland (11)", "attr": { "packageList": "bigmelon,BiocOncoTK,DeepBlueR,genomation,HELP,MEDIPS,MEDME,methylumi,qsea,RnBeads,TurboNorm", "id": "CpGIsland" }, "children": [ ] }, { "data": "DNAMethylation (91)", "attr": { "packageList": "ARRmNormalization,BEAT,BEclear,bigmelon,BiocOncoTK,biscuiteer,BiSeq,BPRMeth,bsseq,bumphunter,cbaf,ChAMP,COCOA,COHCAP,coMET,conumee,DAMEfinder,DeepBlueR,DMRcaller,DMRcate,DMRforPairs,dmrseq,DSS,edgeR,ELMER,EnMCB,ENmix,EpiDISH,epihet,funtooNorm,GAprediction,GEM,Harman,HELP,HIREewas,hummingbird,iCheck,les,lumi,MassArray,MBAmethyl,mCSEA,MEAL,MEAT,MEDIPS,MEDME,Melissa,methimpute,methInheritSim,MethPed,methrix,methVisual,methyAnalysis,MethylAid,methylCC,methylGSA,methylInheritance,methylKit,MethylMix,methylMnM,methylPipe,MethylSeekR,methylSig,methylumi,methyvim,minfi,MIRA,missMethyl,MoonlightR,MPFE,normalize450K,omicsPrint,pathwayPCA,pwrEWAS,qsea,ramwas,recountmethylation,REMP,Repitools,RnBeads,scmeth,sesame,shinyMethyl,skewr,TCGAbiolinks,TCGAbiolinksGUI,TOAST,TransView,tscR,TurboNorm,wateRmelon", "id": "DNAMethylation" }, "children": [ ] }, { "data": "ExonArray (12)", "attr": { "packageList": "AMARETTO,deco,globalSeq,limma,oligo,PECA,puma,regsplice,siggenes,snm,TIN,xps", "id": "ExonArray" }, "children": [ ] }, { "data": "GeneExpression (487)", "attr": { "packageList": "a4Classif,ABAEnrichment,acde,adaptest,ADImpute,AffiXcan,affycoretools,affylmGUI,AffyRNADegradation,AGDEX,aggregateBioVar,AIMS,ALDEx2,alpine,AMARETTO,AMOUNTAIN,Anaquin,anota,anota2seq,antiProfiles,APAlyzer,apeglm,ASpediaFI,ASpli,ASSIGN,attract,AUCell,bambu,BANDITS,BASiCS,batchelor,BayesKnockdown,BayesSpace,BgeeCall,BgeeDB,bigPint,biobroom,bioCancer,BiocOncoTK,BioCor,BiocSet,BioNet,BioNetStat,BioQC,BioTIP,biotmle,BitSeq,blacksheepr,blima,bluster,BPRMeth,BrainSABER,BRGenomics,BUMHMM,BUScorrect,CAFE,CAGEfightR,CAGEr,calm,canceR,CancerInSilico,CancerSubtypes,CARNIVAL,casper,categoryCompare,cbaf,ccmap,CCPROMISE,celda,cellity,CellMapper,CellMixS,CellScore,CellTrails,cellTree,CEMiTool,CeTF,CHARGE,chromswitch,CiteFuse,clustComp,ClusterJudge,clusterSeq,cmapR,CNVRanger,coexnet,CoGAPS,cogena,cola,compEpiTools,CONFESS,consensus,consensusOV,coRdon,CoRegFlux,CoRegNet,coseq,CountClust,covEB,covRNA,CrossICC,crossmeta,ctgGEM,cTRAP,ctsGE,cummeRbund,DART,dcGSA,ddCt,dearseq,debCAM,debrowser,deco,DEComplexDisease,DEFormats,DegNorm,DEGreport,DEGseq,DeMAND,DeMixT,DESeq2,DEsingle,DEsubs,DEXSeq,dexus,diffcoexp,diffuStats,diggit,distinct,dittoSeq,DMRcate,doppelgangR,doseR,DRIMSeq,DropletUtils,DrugVsDisease,DSS,DTA,Dune,EasyqpcR,easyRNASeq,EBSEA,EBSeqHMM,edge,edgeR,eegc,EGSEA,eisa,eisaR,ELBOW,ELMER,EMDomics,EmpiricalBrownsMethod,EnhancedVolcano,EnrichmentBrowser,epigenomix,erccdashboard,ERSSA,ExiMiR,ExpressionView,farms,fastLiquidAssociation,FCBF,fcoex,ffpe,fgsea,fishpond,FoldGO,gage,GAPGOM,GDCRNATools,GEM,geneClassifiers,GeneExpressionSignature,genefu,GeneGA,GeneMeta,GeneTonic,GENIE3,GenomicOZone,GenRank,gep2pep,getDEE2,GGPA,GGtools,GIGSEA,Glimma,globalSeq,GmicR,GNET2,GOexpress,GOpro,goProfiles,goseq,goSTAG,GOstats,GOsummaries,GPA,GRENITS,GRridge,GSALightning,GSCA,GSEABase,GSEABenchmarkeR,gsean,GSgalgoR,GSReg,GWENA,HDTD,hipathia,HIPPO,HPAStainR,HTqPCR,HTSFilter,hummingbird,HybridMTest,iBMQ,icetea,iCheck,ideal,iGC,ILoReg,IMAS,ImpulseDE2,Informeasure,InTAD,interactiveDisplay,interactiveDisplayBase,InterMineR,IntramiRExploreR,iSEE,iSEEu,IsoformSwitchAnalyzeR,ISoLDE,IVAS,ivygapSE,KEGGlincs,KnowSeq,levi,limma,limmaGUI,LINC,LineagePulse,Linnorm,lionessR,LiquidAssociation,loci2path,M3C,M3Drop,made4,mAPKL,massiR,MAST,MBASED,mbkmeans,MBttest,MCbiclust,MEB,Melissa,messina,MetaNeighbor,metaseqR,metaseqR2,MetaVolcanoR,MethReg,MethylMix,mfa,MGFM,MGFR,MIGSA,MiRaGE,miRLAB,miRSM,miRspongeR,mitch,mnem,MODA,mogsa,monocle,MoonlightR,MPRAnalyze,Mulcom,MultiBaC,multiClust,NBAMSeq,Nebulosa,NeighborNet,netbenchmark,netresponse,netSmooth,networkBMA,NewWave,nondetects,NormqPCR,OGSA,oligo,omicplotR,omicRexposome,oncomix,oposSOM,oppar,oppti,Oscope,OUTRIDER,OVESEG,padma,pandaR,pathprint,pathview,pathwayPCA,PCAtools,pcot2,PECA,peco,phantasus,PharmacoGx,phenopath,Pi,piano,Pigengene,pipeComp,plgem,Polyfit,POST,PoTRA,prebs,PrecisionTrialDrawer,PREDA,Prize,proActiv,progeny,PROMISE,PROPS,psichomics,PubScore,puma,qpcrNorm,qpgraph,QuaternaryProd,QUBIC,R3CPET,randRotation,RankProd,RBioinf,Rcade,RCASPAR,rcellminer,ReactomeGSA,ReadqPCR,receptLoss,recount,recount3,recoup,RegEnrich,regutools,Repitools,RIVER,RmiR,Rmmquant,RNAAgeCalc,RNAdecay,RNAsense,rnaSeqMap,RNASeqR,RnaSeqSampleSize,Rnits,ROSeq,ROTS,RPA,rScudo,Rsubread,RTCGAToolbox,RTN,RTNduals,runibic,RUVcorr,SAGx,samExploreR,sampleClassifier,sarks,SBGNview,scater,scBFA,SCBN,scCB2,scClassify,scDataviz,scds,scFeatureFilter,scHOT,scMAGeCK,scmap,scMerge,scone,scp,scPCA,scPipe,scran,scRecover,scry,scTensor,scTGIF,scuttle,SEPIRA,SeqGate,SeqGSEA,SEtools,sigaR,SigCheck,sigFeature,siggenes,signatureSearch,signet,SIMLR,sincell,singleCellTK,SingleR,singscore,slalom,slingshot,slinky,snapcount,snm,Spaniel,SpatialDecon,spatialHeatmap,splatter,SplicingGraphs,splineTimeR,SPLINTER,SPONGE,SPsimSeq,sRACIPE,srnadiff,sscu,SSPA,ssPATHS,STROMA4,subSeq,supraHex,survcomp,survtype,SVAPLSseq,switchde,systemPipeR,TBSignatureProfiler,TCGAbiolinks,TCGAbiolinksGUI,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,tigre,TimeSeriesExperiment,TIN,TissueEnrich,TMixClust,TNBC.CMS,TOAST,tomoda,ToPASeq,topconfects,ToxicoGx,tradeSeq,transcriptogramer,transite,tRanslatome,TransView,trena,trigger,TSCAN,tscR,TSRchitect,tximeta,tximport,unifiedWMWqPCR,variancePartition,velociraptor,vidger,viper,vulcan,weitrix,wiggleplotr,Xeva,xps,yarn,zFPKM,zinbwave", "id": "GeneExpression" }, "children": [ ] }, { "data": "GeneticVariability (45)", "attr": { "packageList": "appreci8R,BBCAnalyzer,beadarraySNP,BiocOncoTK,BUMHMM,CAnD,chopsticks,Clomial,CNVtools,CrispRVariants,deepSNV,FRGEpistasis,GeneAccord,GeneGeneInteR,GENESIS,GGtools,gmoviz,GSReg,GWASTools,gwasurvivr,hapFabia,ISoLDE,martini,metagenomeSeq,microbiomeExplorer,missMethyl,OMICsPCA,omicsPrint,pathVar,phyloseq,qpgraph,QSutils,Rgin,RIVER,RLMM,Rsubread,RTN,samExploreR,SeqVarTools,SIAMCAT,snpStats,trigger,trio,TVTB,VariantTools", "id": "GeneticVariability" }, "children": [ ] }, { "data": "SNP (82)", "attr": { "packageList": "appreci8R,ASAFE,BBCAnalyzer,beadarraySNP,BiocOncoTK,BSgenome,CAnD,CGEN,chopsticks,CNVRanger,CNVrd2,copynumber,crlmm,customProDB,decompTumor2Sig,deepSNV,DRIMSeq,ensemblVEP,gcatest,GEM,geneAttribution,GeneGeneInteR,GeneRegionScan,GENESIS,GenomicAlignments,genoset,genotypeeval,GenRank,GGPA,GGtools,GIGSEA,GMRP,GPA,GWAS.BAYES,GWASTools,gwasurvivr,hapFabia,hierGWAS,hierinf,iASeq,iBMQ,iCNV,IMAS,INPower,InterMineR,inveRsion,ISoLDE,IVAS,lfa,logicFS,martini,MassArray,mBPCR,metaCCA,MinimumDistance,MouseFM,oligo,OPWeight,pathwayPCA,qpgraph,Qtlizer,REBET,Rgin,RIVER,RLMM,Rsubread,sangerseqR,sapFinder,scoreInvHap,semisup,SeqVarTools,SICtools,siggenes,SigsPack,sitePath,SNPediaR,snpStats,systemPipeR,trigger,trio,VariantAnnotation,VariantFiltering", "id": "SNP" }, "children": [ ] }, { "data": "Transcription (158)", "attr": { "packageList": "AffiXcan,affylmGUI,aggregateBioVar,alpine,ALPS,altcdfenvs,AMARETTO,annmap,ASpediaFI,ASpli,AUCell,BAC,bambu,BANDITS,BicARE,BiFET,bigPint,BiocOncoTK,BioTIP,BitSeq,blacksheepr,BRGenomics,BUMHMM,CAGEfightR,CAGEr,casper,cbaf,ccmap,CellScore,CeTF,CexoR,ChIPanalyser,ChIPComp,ChIPexoQual,ChIPSeqSpike,chromswitch,CoGAPS,consensusSeekeR,CoRegFlux,CoRegNet,covRNA,crossmeta,CSAR,ctsGE,customProDB,DBChIP,dearseq,deco,DEFormats,DepecheR,DESeq2,diffcoexp,distinct,dpeak,DTA,edgeR,eisaR,ELMER,EnhancedVolcano,enrichTF,erccdashboard,ERSSA,EventPointer,ExiMiR,fCCAC,fishpond,GeneTonic,GenomicOZone,GOexpress,goseq,GSALightning,GSgalgoR,GSRI,Guitar,Harman,icetea,ILoReg,IMAS,InPAS,iSEE,iSEEu,IsoformSwitchAnalyzeR,ISoLDE,IVAS,ivygapSE,les,limma,Linnorm,M3C,MBASED,MBttest,metaseqR2,MethReg,mosaics,motifcounter,MultiBaC,NarrowPeaks,netresponse,OMICsPCA,omicsPrint,pandaR,pathprint,pathwayPCA,PCAtools,primirTSS,proActiv,psichomics,pwOmics,qpgraph,QuaternaryProd,Rcade,RcisTarget,RegEnrich,regionReport,regutools,RIVER,Rmmquant,RNAdecay,rnaSeqMap,roar,RRHO,RTN,rTRM,rTRMui,SC3,scDataviz,scde,scmap,SELEX,SEPIRA,SGSeq,sigFeature,simpleaffy,snm,SplicingGraphs,SPONGE,STAN,subSeq,target,TFARM,TFBSTools,TFEA.ChIP,TFHAZ,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,tigre,TimeSeriesExperiment,transcriptogramer,transcriptR,transite,TransView,trena,TSRchitect,tximeta,tximport,wiggleplotr,xps", "id": "Transcription" }, "children": [ ] } ] }, { "data": "BiologicalQuestion (823)", "attr": { "packageList": "ChIPanalyser,consensusSeekeR,decompTumor2Sig,deltaCaptureC,discordant,GSALightning,INDEED,LINC,methInheritSim,methylInheritance,MetID,musicatk,NoRCE,OMICsPCA,OncoSimulR,projectR,rexposome,RJMCMCNucleosomes,similaRpeak,TFARM,TFHAZ,VplotR,YAPSA", "id": "BiologicalQuestion" }, "children": [ { "data": "AlternativeSplicing (43)", "attr": { "packageList": "alpine,AMARETTO,ASpediaFI,ASpli,BANDITS,BitSeq,customProDB,dasper,DEXSeq,DRIMSeq,edgeR,erccdashboard,EventPointer,fishpond,FRASER,GeneStructureTools,GSReg,IMAS,InPAS,IntEREst,InterMineR,IsoformSwitchAnalyzeR,IVAS,kissDE,limma,maser,MBttest,metaseqR2,NBSplice,PAIRADISE,PathwaySplice,proActiv,psichomics,puma,regsplice,SGSeq,SplicingGraphs,SPLINTER,TIN,Ularcirc,vasp,VaSP,wiggleplotr", "id": "AlternativeSplicing" }, "children": [ ] }, { "data": "Coverage (137)", "attr": { "packageList": "ACE,alpine,animalcules,ASpediaFI,ASpli,ATACseqQC,BadRegionFinder,bambu,bamsignals,Basic4Cseq,BasicSTARRseq,BBCAnalyzer,BPRMeth,brainflowprobes,breakpointR,BRGenomics,BubbleTree,BUMHMM,CAGEfightR,CeTF,ChIPanalyser,ChIPComp,ChIPexoQual,chipseq,ChIPSeqSpike,CNAnorm,CNVPanelizer,CNVrd2,compEpiTools,consensusSeekeR,CopyNumberPlots,CopywriteR,csaw,DAMEfinder,dasper,DegNorm,DeMixT,derfinder,DEScan2,diffcoexp,diffHic,DMCFB,DMCHMM,DMRcaller,DMRcate,DropletUtils,edgeR,EnrichedHeatmap,ensembldb,esATAC,exomePeak2,fCCAC,FRASER,geneXtendeR,GenomicAlignments,GenomicFiles,GenomicOZone,GenomicRanges,GenomicScores,gmoviz,GreyListChIP,HDF5Array,HelloRanges,HilbertCurve,Imetagene,InPAS,IntEREst,karyoploteR,loci2path,MADSEQ,MBttest,MDTS,MEDIPS,megadepth,Melissa,metagene,metagene2,methimpute,methrix,methylPipe,MIRA,NBAMSeq,NewWave,nucleR,openPrimeR,ORFik,periodicDNA,plyranges,profileplyr,PureCN,QuasR,ramwas,RCAS,recount,recount3,recoup,regionReport,RepViz,restfulSE,rGREAT,RiboProfiling,ribosomeProfilingQC,RJMCMCNucleosomes,RNAprobR,Rsamtools,runibic,Scale4C,scater,scGPS,scone,SCOPE,seqCAT,sevenC,SICtools,signatureSearch,SMITE,snapcount,soGGi,Spaniel,srnadiff,strandCheckR,SummarizedExperiment,survtype,systemPipeR,TarSeqQC,TFHAZ,topdownr,transcriptR,traseR,TVTB,Ularcirc,UMI4Cats,uncoverappLib,velociraptor,VplotR,wiggleplotr,XCIR", "id": "Coverage" }, "children": [ ] }, { "childnum": 0, "data": "DemethylateRegionDetection", "children": [ ] }, { "childnum": 0, "data": "DenovoAssembler", "children": [ ] }, { "data": "DifferentialExpression (339)", "attr": { "packageList": "ABSSeq,acde,adaptest,AffyExpress,affylmGUI,aggregateBioVar,AgiMicroRna,ALDEx2,AMARETTO,AMOUNTAIN,Anaquin,ANCOMBC,anota,anota2seq,APAlyzer,apeglm,ArrayTools,artMS,ASpli,BADER,ballgown,bambu,BANDITS,BASiCS,BatchQC,baySeq,BGmix,bgx,bigPint,biobroom,BioNet,BioNetStat,biotmle,BitSeq,blacksheepr,blima,BLMA,bridge,calm,casper,CATALYST,CausalR,ccmap,CellTrails,CeTF,circRNAprofiler,clippda,clusterSeq,CNVRanger,coexnet,CoGAPS,coGPS,compcodeR,consensusOV,copa,Cormotif,cqn,CrossICC,crossmeta,ctgGEM,cTRAP,ctsGE,cummeRbund,daMA,DART,dcanr,ddCt,dearseq,debrowser,deco,DEComplexDisease,DeconRNASeq,DEFormats,DegNorm,DEGraph,DEGreport,DEGseq,DEP,DepecheR,DEqMS,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEsingle,DEsubs,DEWSeq,DEXSeq,dexus,DFP,diffcoexp,diffGeneAnalysis,distinct,DMRcate,doseR,DRIMSeq,DSS,DTA,EBarrays,EBSEA,EBSeq,EBSeqHMM,EDASeq,edge,edgeR,eegc,EGSEA,EMDomics,EnhancedVolcano,EnrichmentBrowser,epigenomix,erccdashboard,ERSSA,exomePeak2,ExploreModelMatrix,fabia,factDesign,fdrame,fgsea,fishpond,flagme,FoldGO,gaga,gage,gCrisprTools,GCSscore,GDCRNATools,genefu,GeneSelectMMD,geNetClassifier,GeneTonic,GenoGAM,GenomicOZone,gep2pep,GGPA,GIGSEA,Glimma,GlobalAncova,globalSeq,globaltest,GOexpress,goSTAG,GPA,gprege,GSALightning,GSAR,GSEABenchmarkeR,gsean,GSRI,HDTD,HEM,HIPPO,HTqPCR,HTSFilter,hummingbird,icetea,iCheck,ideal,iGC,IgGeneUsage,ILoReg,IMAS,ImpulseDE2,INDEED,IntEREst,InterMineR,IsoformSwitchAnalyzeR,IsoGeneGUI,isomiRs,IVAS,IWTomics,JunctionSeq,KnowSeq,lapmix,lefser,les,limma,limmaGUI,LineagePulse,Linnorm,lmdme,logitT,LPE,M3Drop,maanova,macat,maigesPack,mAPKL,MAST,MBttest,MEB,MEDIPS,messina,metaArray,metagenomeSeq,metahdep,metaSeq,metaseqR,metaseqR2,MetaVolcanoR,MethylMix,microbiomeExplorer,miRNApath,mitch,MmPalateMiRNA,MODA,MOGAMUN,monocle,MoonlightR,MPRAnalyze,MSstatsPTM,MSstatsSampleSize,MSstatsTMTPTM,Mulcom,multtest,muscat,NanoStringDiff,NBAMSeq,NBSplice,netresponse,NOISeq,NoRCE,NormalyzerDE,OCplus,oligo,omicplotR,omicRexposome,oposSOM,oppti,OrderedList,PAIRADISE,PathNet,pathview,pcot2,PECA,phantasus,phenoTest,piano,pickgene,plgem,PLPE,polyester,Polyfit,PoTRA,proDA,PROPER,ProteoMM,psichomics,puma,QUBIC,randRotation,RankProd,RBM,Rcade,RDAVIDWebService,recount,recount3,RegEnrich,regionReport,regsplice,rgsepd,RNAdecay,RNAsense,rnaSeqMap,RNASeqR,RnaSeqSampleSize,Rnits,ROC,ROSeq,ROTS,rScudo,RTCGAToolbox,RUVSeq,safe,SAGx,sarks,SBGNview,SC3,SCBN,scDD,scde,scPCA,SDAMS,segmentSeq,SeqGate,SeqGSEA,sigaR,siggenes,signatureSearch,signet,sigPathway,SIMD,similaRpeak,simpleaffy,singleCellTK,slingshot,slinky,SMITE,snm,SpeCond,splineTimeR,srnadiff,sscore,ssize,statTarget,subSeq,survcomp,switchde,TBSignatureProfiler,TCC,TCGAbiolinks,TCGAbiolinksGUI,TCseq,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,timecourse,TimeSeriesExperiment,TOAST,ToPASeq,topconfects,tradeSeq,transcriptogramer,transite,tRanslatome,TTMap,tweeDEseq,twilight,unifiedWMWqPCR,variancePartition,vasp,VaSP,vidger,waddR,webbioc,XBSeq,XDE,xps", "id": "DifferentialExpression" }, "children": [ ] }, { "data": "DifferentialMethylation (44)", "attr": { "packageList": "AMARETTO,ChIPSeqSpike,COHCAP,coMET,DAMEfinder,DMCFB,DMCHMM,DMRcaller,DMRcate,DMRforPairs,dmrseq,DSS,edgeR,ENmix,EpiDISH,GenomicOZone,HIREewas,hummingbird,IWTomics,mCSEA,MethCP,methInheritSim,methylGSA,methylInheritance,MethylMix,methylSig,methyvim,minfi,missMethyl,MoonlightR,msgbsR,NanoMethViz,omicRexposome,pwrEWAS,qsea,ramwas,regionReport,REMP,RnBeads,SIMD,SMITE,TCGAbiolinks,TCGAbiolinksGUI,TOAST", "id": "DifferentialMethylation" }, "children": [ ] }, { "data": "DifferentialPeakCalling (14)", "attr": { "packageList": "ChromSCape,chromstaR,chromswitch,csaw,CSSQ,derfinder,DiffBind,geneXtendeR,GenoGAM,GreyListChIP,IWTomics,MMDiff2,normr,regionReport", "id": "DifferentialPeakCalling" }, "children": [ ] }, { "data": "DifferentialSplicing (34)", "attr": { "packageList": "alpine,AMARETTO,ASpli,BANDITS,BitSeq,DEXSeq,DRIMSeq,edgeR,erccdashboard,EventPointer,ExCluster,fishpond,GeneStructureTools,IMAS,InPAS,IntEREst,IsoformSwitchAnalyzeR,IVAS,kissDE,limma,MBttest,metaseqR2,NBSplice,PathwaySplice,PECA,proActiv,psichomics,puma,regsplice,SeqGSEA,TIN,Ularcirc,vasp,VaSP", "id": "DifferentialSplicing" }, "children": [ ] }, { "data": "DNA3DStructure (5)", "attr": { "packageList": "DNAshapeR,FitHiC,idr2d,MACPET,sevenC", "id": "DNA3DStructure" }, "children": [ ] }, { "data": "DriverMutation (1)", "attr": { "packageList": "maftools", "id": "DriverMutation" }, "children": [ ] }, { "data": "FunctionalPrediction (20)", "attr": { "packageList": "BasicSTARRseq,circRNAprofiler,diggit,drawProteins,EGAD,famat,garfield,GeneStructureTools,GenomicOZone,InterMineR,IsoformSwitchAnalyzeR,OmaDB,PCAN,PhyloProfile,progeny,projectR,RegEnrich,RIVER,RNASeqR,viper", "id": "FunctionalPrediction" }, "children": [ ] }, { "data": "GeneFusionDetection (1)", "attr": { "packageList": "Rsubread", "id": "GeneFusionDetection" }, "children": [ ] }, { "data": "GenePrediction (19)", "attr": { "packageList": "AssessORF,circRNAprofiler,coRdon,CoRegFlux,DECIPHER,EGAD,GAPGOM,geneAttribution,GRridge,IntramiRExploreR,IsoformSwitchAnalyzeR,mixOmics,MouseFM,pathwayPCA,R3CPET,RandomWalkRestartMH,sigFeature,timeOmics,TNBC.CMS", "id": "GenePrediction" }, "children": [ ] }, { "data": "GeneRegulation (94)", "attr": { "packageList": "AffiXcan,AMARETTO,anota2seq,APAlyzer,ATACseqQC,BasicSTARRseq,BCRANK,BiFET,blima,BPRMeth,BRGenomics,BUMHMM,CAGEfightR,chromVAR,cicero,cleanUpdTSeq,CNEr,COCOA,CoRegFlux,CoRegNet,CRISPRseek,crisprseekplus,DeepBlueR,DEWSeq,diggit,eegc,eisaR,ELMER,GDCRNATools,geneplast,GenomicOZone,GIGSEA,GRENITS,GSReg,GSRI,GUIDEseq,idr2d,IMAS,InPAS,INSPEcT,InterMineR,ISoLDE,IVAS,LINC,LOLA,MatrixRider,Melissa,methylGSA,MethylMix,MIRA,miRSM,MoonlightR,mpra,NADfinder,omicRexposome,OmnipathR,pandaR,pqsfinder,primirTSS,proActiv,profileScoreDist,progeny,projectR,qpgraph,RcisTarget,regutools,ribosomeProfilingQC,RIVER,RNAdecay,Rsubread,RTN,RTNduals,RTNsurvival,rTRM,rTRMui,samExploreR,sarks,SELEX,SEPIRA,SpidermiR,SPONGE,sRACIPE,StarBioTrek,TCGAbiolinks,TCGAbiolinksGUI,TFBSTools,TFEA.ChIP,tigre,tRanslatome,trena,triplex,TSRchitect,universalmotif,viper", "id": "GeneRegulation" }, "children": [ ] }, { "data": "GeneSetEnrichment (131)", "attr": { "packageList": "ABAEnrichment,ADAM,ADAMgui,AMARETTO,artMS,ASpediaFI,attract,AUCell,BgeeDB,BioNetStat,BioQC,BLMA,CAFE,Category,cellTree,chipenrich,ChromSCape,clusterProfiler,CoGAPS,cogena,CompGO,coRdon,cpvSNP,CrossICC,cTRAP,ctsGE,dcGSA,dearseq,DOSE,edgeR,eegc,EGSEA,EnrichmentBrowser,enrichplot,escape,famat,FGNet,fgsea,gage,gCrisprTools,GDCRNATools,GeneTonic,gep2pep,GIGSEA,GISPA,GOexpress,GOfuncR,GOFunction,GOpro,goProfiles,goSTAG,GOstats,GRridge,GSALightning,GSEABase,GSEABenchmarkeR,GSEAmining,gsean,GSReg,GSRI,GSVA,GWENA,HPAStainR,hypeR,iBBiG,ideal,InterMineR,ISoLDE,KnowSeq,limma,loci2path,LOLA,MAGeCKFlute,MAST,mdgsa,metaseqR2,methylGSA,mgsa,MIGSA,miRSM,missMethyl,mitch,MoonlightR,multiGSEA,netboxr,NoRCE,npGSEA,oposSOM,oppar,PAST,pathVar,pathview,pathwayPCA,PathwaySplice,paxtoolsr,piano,PloGO2,PPInfer,PubScore,qusage,RCAS,RcisTarget,ReactomeGSA,ReactomePA,RegEnrich,ReportingTools,rGREAT,RGSEA,rgsepd,RITAN,RNASeqR,RTN,RTNsurvival,safe,SAGx,SBGNview,SeqGSEA,SigCheck,simplifyEnrichment,sincell,singscore,SISPA,slinky,splineTimeR,systemPipeR,TFEA.ChIP,TissueEnrich,transcriptogramer,transite,variancePartition,ViSEAGO", "id": "GeneSetEnrichment" }, "children": [ ] }, { "data": "GeneSignaling (8)", "attr": { "packageList": "EGSEA,escape,hipathia,MetaboSignal,OmnipathR,pathwayPCA,pwOmics,RankProd", "id": "GeneSignaling" }, "children": [ ] }, { "data": "GeneTarget (35)", "attr": { "packageList": "BayesKnockdown,bioCancer,brainflowprobes,cicero,distinct,eegc,EGSEA,enrichTF,FCBF,GDCRNATools,gespeR,IntramiRExploreR,MAGeCKFlute,MetaboSignal,MethReg,miRSM,MouseFM,networkBMA,NoRCE,Onassis,oppti,pageRank,pathwayPCA,Pi,pwOmics,RCAS,RcisTarget,RegEnrich,rnaEditr,samExploreR,SBGNview,SEPIRA,spatialHeatmap,sRACIPE,TOAST", "id": "GeneTarget" }, "children": [ ] }, { "data": "GenomeAnnotation (45)", "attr": { "packageList": "AnnotationDbi,annotatr,ASpli,AssessORF,atSNP,bambu,branchpointer,COCOA,compEpiTools,DeepBlueR,DelayedArray,DMRcate,EnrichedHeatmap,fcScan,garfield,geneXtendeR,GenomeInfoDb,GenomicFeatures,GenomicRanges,GreyListChIP,HDF5Array,HelloRanges,HilbertCurve,InterMineR,IWTomics,LOLA,mCSEA,MEDIPS,microRNA,MIRA,NoRCE,Organism.dplyr,QDNAseq,RCAS,rGREAT,RNAprobR,Rsubread,samExploreR,scPipe,SMITE,STAN,SummarizedExperiment,TSRchitect,tximeta,VariantExperiment", "id": "GenomeAnnotation" }, "children": [ ] }, { "data": "GenomeAssembly (5)", "attr": { "packageList": "bambu,circRNAprofiler,contiBAIT,nanotatoR,NoRCE", "id": "GenomeAssembly" }, "children": [ ] }, { "data": "GenomeWideAssociation (30)", "attr": { "packageList": "anota2seq,ASAFE,bacon,CNVRanger,coMET,diffuStats,gcatest,GEM,geneAttribution,GeneGeneInteR,GENESIS,genphen,GGPA,GISPA,globalSeq,GPA,gwasurvivr,hierinf,iCARE,InterMineR,martini,metaCCA,pathwayPCA,Pi,Qtlizer,REMP,Rgin,rqt,RVS,SISPA", "id": "GenomeWideAssociation" }, "children": [ ] }, { "data": "GenomicVariation (36)", "attr": { "packageList": "AneuFinder,branchpointer,CINdex,CNAnorm,CNVRanger,COCOA,cpvSNP,CrispRVariants,decompTumor2Sig,FindMyFriends,GeneAccord,geneAttribution,GenomicOZone,gmoviz,iGC,infercnv,ipdDb,kissDE,MADSEQ,missMethyl,MouseFM,myvariant,panelcn.mops,pathwayPCA,RareVariantVis,Rariant,RepViz,RIVER,scoreInvHap,semisup,seqCAT,signeR,SomaticSignatures,TitanCNA,TVTB,YAPSA", "id": "GenomicVariation" }, "children": [ ] }, { "childnum": 0, "data": "GermlineMutation", "children": [ ] }, { "data": "HistoneModification (6)", "attr": { "packageList": "ALPS,chipenrich,ChIPSeqSpike,chromstaR,chromswitch,geneXtendeR", "id": "HistoneModification" }, "children": [ ] }, { "data": "IndelDetection (1)", "attr": { "packageList": "Rsubread", "id": "IndelDetection" }, "children": [ ] }, { "data": "LinkageDisequilibrium (6)", "attr": { "packageList": "ASAFE,CNVrd2,hierGWAS,hierinf,Pi,Qtlizer", "id": "LinkageDisequilibrium" }, "children": [ ] }, { "childnum": 0, "data": "MetagenomeAssembly", "children": [ ] }, { "childnum": 0, "data": "MicrosatelliteDetection", "children": [ ] }, { "data": "MotifAnnotation (21)", "attr": { "packageList": "atSNP,branchpointer,coMET,DiffLogo,ELMER,enrichTF,LedPred,MatrixRider,motifbreakR,motifcounter,MotifDb,motifmatchr,motifStack,MotIV,periodicDNA,PWMEnrich,RCAS,RcisTarget,SELEX,TFBSTools,universalmotif", "id": "MotifAnnotation" }, "children": [ ] }, { "data": "MotifDiscovery (10)", "attr": { "packageList": "BCRANK,nearBynding,periodicDNA,pqsfinder,RCAS,rGADEM,sarks,SELEX,TFBSTools,universalmotif", "id": "MotifDiscovery" }, "children": [ ] }, { "data": "NetworkEnrichment (40)", "attr": { "packageList": "BioCor,BioNet,CEMiTool,CoRegNet,DEGraph,DeMAND,DEsubs,diggit,EGAD,EGSEA,EnrichmentBrowser,fcoex,FELLA,FGNet,GDCRNATools,GSEABenchmarkeR,gsean,GWENA,ibh,miRNApath,miRspongeR,MOMA,MoonlightR,netboxr,PathNet,PathwaySplice,paxtoolsr,PPInfer,RegEnrich,RITAN,RTN,RTNduals,RTNsurvival,signatureSearch,signet,SMITE,splineTimeR,ToPASeq,viper,vulcan", "id": "NetworkEnrichment" }, "children": [ ] }, { "data": "NetworkInference (56)", "attr": { "packageList": "apComplex,ASpediaFI,BayesKnockdown,BioNetStat,ceRNAnetsim,cliqueMS,CNORfeeder,coexnet,CoRegNet,CytoTree,dcanr,epiNEM,flowSpy,FRGEpistasis,GDCRNATools,GENIE3,GmicR,GNET2,GRENITS,Informeasure,joda,KEGGlincs,lionessR,lpNet,minet,miRLAB,mnem,MOMA,netbenchmark,netresponse,networkBMA,pandaR,PANR,Path2PPI,Pigengene,ppiStats,predictionet,PrInCE,qpgraph,R3CPET,RandomWalkRestartMH,RegEnrich,regutools,RITAN,RTN,RTNduals,RTNsurvival,ScISI,SEPIRA,SPEM,splineTimeR,SPONGE,spqn,tigre,trena,TRONCO", "id": "NetworkInference" }, "children": [ ] }, { "data": "NucleosomePositioning (5)", "attr": { "packageList": "ATACseqQC,nucleR,nuCpos,RJMCMCNucleosomes,VplotR", "id": "NucleosomePositioning" }, "children": [ ] }, { "data": "PeakDetection (16)", "attr": { "packageList": "BasicSTARRseq,CAGEfightR,ChIPanalyser,chromstaR,consensusSeekeR,DEScan2,gcapc,geneXtendeR,idr2d,Linnorm,MACPET,NADfinder,normr,PeacoQC,peakPantheR,proFIA", "id": "PeakDetection" }, "children": [ ] }, { "childnum": 0, "data": "QuantitativeTrailLocus", "children": [ ] }, { "childnum": 0, "data": "Scaffolding", "children": [ ] }, { "data": "SequenceMatching (48)", "attr": { "packageList": "Basic4Cseq,bcSeq,Biostrings,BSgenome,ChIPanalyser,cleanUpdTSeq,CRISPRseek,crisprseekplus,dagLogo,DiffLogo,DominoEffect,FastqCleaner,FindMyFriends,FunciSNP,genphen,hapFabia,heatmaps,HelloRanges,IMMAN,ipdDb,KinSwingR,Logolas,LowMACA,MEDIPS,MethTargetedNGS,microRNA,MmPalateMiRNA,motifcounter,motifStack,muscle,packFinder,periodicDNA,pqsfinder,PWMEnrich,QSutils,REDseq,RRHO,Rsubread,samExploreR,scPipe,seqLogo,seqPattern,SICtools,SimFFPE,Structstrings,SynMut,triplex,TVTB", "id": "SequenceMatching" }, "children": [ ] }, { "data": "SomaticMutation (24)", "attr": { "packageList": "decompTumor2Sig,DominoEffect,GeneAccord,HiLDA,LACE,LowMACA,MADSEQ,maftools,musicatk,MutationalPatterns,OncoSimulR,PrecisionTrialDrawer,QuartPAC,RandomWalkRestartMH,Rariant,selectKSigs,semisup,signeR,SigsPack,SomaticSignatures,SparseSignatures,TRONCO,VERSO,YAPSA", "id": "SomaticMutation" }, "children": [ ] }, { "data": "SplicedAlignment (2)", "attr": { "packageList": "Guitar,Rhisat2", "id": "SplicedAlignment" }, "children": [ ] }, { "data": "StructuralVariation (3)", "attr": { "packageList": "FilterFFPE,GenomicOZone,infercnv", "id": "StructuralVariation" }, "children": [ ] }, { "data": "TranscriptomeVariant (2)", "attr": { "packageList": "IsoformSwitchAnalyzeR,RIVER", "id": "TranscriptomeVariant" }, "children": [ ] }, { "data": "VariantAnnotation (25)", "attr": { "packageList": "appreci8R,cellbaseR,ensemblVEP,geneAttribution,genotypeeval,GIGSEA,HelloRanges,ipdDb,maftools,MouseFM,musicatk,myvariant,nanotatoR,PCAN,podkat,PureCN,REBET,Rsubread,seqCAT,SigsPack,SNPediaR,StructuralVariantAnnotation,TVTB,VariantAnnotation,VCFArray", "id": "VariantAnnotation" }, "children": [ ] }, { "data": "VariantDetection (11)", "attr": { "packageList": "appreci8R,CrispRVariants,infercnv,MADSEQ,MMAPPR2,panelcn.mops,PureCN,Rariant,Rsubread,RVS,SICtools", "id": "VariantDetection" }, "children": [ ] } ] }, { "data": "Infrastructure (455)", "attr": { "packageList": "affxparser,AffyCompatible,affyContam,affyio,AllelicImbalance,AnnotationFilter,AnnotationForge,AnnotationHub,AnVIL,AnVILBilling,AnVILPublish,aroma.light,arrayMvout,basecallQC,BaseSpaceR,basilisk,basilisk.utils,beachmat,bigmemoryExtras,bioassayR,Biobase,BiocCaseStudies,BiocCheck,BiocDockerManager,BiocGenerics,BiocParallel,BiocPkgTools,BiocSklearn,BiocVersion,biocViews,BioMVCClass,Biostrings,biovizBase,BSgenome,BufferedMatrix,BufferedMatrixMethods,bumphunter,Cardinal,cBioPortalData,CellBench,CGHbase,ChemmineOB,ChemmineR,chimera,chimeraviz,ChIPseqR,ChIPsim,convert,cummeRbund,DelayedArray,DelayedDataFrame,DelayedMatrixStats,doseR,DynDoc,eiR,ENCODExplorer,epivizr,epivizrData,epivizrServer,epivizrStandalone,ExperimentHub,ExperimentHubData,ExperimentSubset,flowBeads,flowcatchR,flowCore,FlowRepositoryR,flowUtils,flowViz,fmcsR,FunciSNP,GCSConnection,GCSFilesystem,GDSArray,gdsfmt,genbankr,GeneAnswers,genomeIntervals,GenomicAlignments,GenomicFeatures,GenomicFiles,GenomicInteractions,GenomicRanges,GenomicScores,GenomicTuples,genoset,GenVisR,GEOmetadb,GGBase,ggbio,ggcyto,gpuMagic,HCAMatrixBrowser,HDF5Array,Herper,HiCBricks,hmdbQuery,HumanTranscriptomeCompendium,Icens,illuminaio,InteractionSet,IRanges,LoomExperiment,lpsymphony,LRBaseDbi,MatrixGenerics,matter,MeSHDbi,metagenomeFeatures,metavizr,MetID,microRNA,mimager,Modstrings,monocle,MsCoreUtils,MSEADbi,MSnbase,MultiAssayExperiment,MVCClass,mzR,oligoClasses,ontoProc,OrganismDbi,panp,pdInfoBuilder,pipeFrame,pkgDepTools,plyranges,preprocessCore,ProtGenerics,psygenet2r,QFeatures,R453Plus1Toolbox,RaggedExperiment,rebook,RedeR,restfulSE,rexposome,RGalaxy,RGMQL,rhdf5,rhdf5filters,Rhdf5lib,ribor,RNAmodR,RNAmodR.ML,RNASeqR,RProtoBufLib,RpsiXML,rRDP,RSeqAn,RTCA,S4Vectors,scater,SeqArray,SharedObject,SingleCellExperiment,SNPRelate,Spaniel,sparseMatrixStats,SpatialExperiment,Spectra,SQLDataFrame,SRAdb,ssrch,Streamer,Structstrings,SummarizedBenchmark,SummarizedExperiment,Sushi,systemPipeR,systemPipeShiny,TFARM,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,TileDBArray,tkWidgets,TnT,tofsims,topdownr,TreeAndLeaf,TreeSummarizedExperiment,TypeInfo,UniProt.ws,VariantExperiment,VCFArray,weaver,webbioc,widgetTools,XVector,zlibbioc", "id": "Infrastructure" }, "children": [ { "data": "DataImport (227)", "attr": { "packageList": "aCGH,adductomicsR,affxparser,affyio,affylmGUI,AlpsNMR,AMARETTO,AnnotationHub,AnnotationHubData,APAlyzer,ArrayExpress,ASICS,bamsignals,basecallQC,BaseSpaceR,Basic4Cseq,BayesSpace,beachmat,beadarraySNP,BgeeDB,bigmelon,bigPint,bioassayR,biobroom,BiocFileCache,BiocIO,biomformat,BioNet,Biostrings,biscuiteer,BrainStars,brendaDb,BRGenomics,CAGEfightR,CellScore,ChemmineOB,ChemmineR,ChIPanalyser,ChIPComp,chipseq,ChIPSeqSpike,cmapR,CNEr,CNVfilteR,codelink,cogena,CONFESS,CopyNumberPlots,ctc,ctgGEM,cummeRbund,cytolib,cytomapper,CytoML,DAPAR,DECIPHER,DeepBlueR,deepSNV,DegNorm,diffloop,dittoSeq,DMRcate,Doscheda,DropletUtils,edge,eiR,ENCODExplorer,ENmix,ExperimentHub,ExperimentHubData,ExperimentSubset,flowSpecs,flowTime,flowWorkspace,fmcsR,FunciSNP,gaggle,GCSscore,gdsfmt,gemini,genbankr,GeneRegionScan,geneXtendeR,genomeIntervals,GenomicAlignments,GenomicDataCommons,GenomicFiles,GenomicInteractions,genotypeeval,GEOquery,ggtree,Guitar,HCABrowser,HCAExplorer,HDF5Array,HelloRanges,HELP,HiCBricks,HTqPCR,ibh,illuminaio,ImmuneSpaceR,IONiseR,IsoformSwitchAnalyzeR,IWTomics,karyoploteR,KnowSeq,limma,limmaGUI,LOBSTAHS,LoomExperiment,LowMACA,MACSQuantifyR,makecdfenv,MANOR,MassArray,MDTS,megadepth,metaseqR2,MethTargetedNGS,minfi,Modstrings,monocle,motifStack,msgbsR,MSnbase,MSstatsConvert,muscle,mzID,mzR,ncRNAtools,ndexr,normr,nucleR,oligo,OmnipathR,Onassis,openCyto,ORFik,OTUbase,PepsNMR,periodicDNA,plethy,plotGrouper,podkat,PrecisionTrialDrawer,profileplyr,ProteomicsAnnotationHubData,PSICQUIC,psygenet2r,puma,qPLEXanalyzer,qrqc,QSutils,R453Plus1Toolbox,R4RNA,Rcpi,RcwlPipelines,ReadqPCR,recount,recount3,recoup,REMP,rexposome,rfaRm,RGMQL,rhdf5,rhdf5client,rhdf5filters,Rhtslib,RImmPort,Ringo,Risa,RNASeqR,RnBeads,rpx,Rqc,Rsamtools,RTCGA,Rtpca,rtracklayer,SAGx,Scale4C,scater,scCB2,scDataviz,scGPS,scmap,SCOPE,scuttle,segmentSeq,sevenbridges,sevenC,ShortRead,SICtools,SimFFPE,simpleaffy,SingleCellExperiment,slinky,snapcount,Spaniel,SpatialExperiment,SRAdb,Starr,Streamer,Structstrings,StructuralVariantAnnotation,SynExtend,systemPipeR,systemPipeShiny,TarSeqQC,tofsims,TPP2D,transomics2cytoscape,TransView,traseR,treeio,tRNAdbImport,tRNAscanImport,TRONCO,TVTB,tximeta,tximport,universalmotif,VariantAnnotation,xps,zellkonverter", "id": "DataImport" }, "children": [ ] }, { "data": "DataRepresentation (112)", "attr": { "packageList": "BaseSpaceR,beachmat,bigmemoryExtras,bioCancer,Biostrings,BSgenome,CAGEfightR,CellTrails,chromPlot,cmapR,cogena,consensus,CrispRVariants,cummeRbund,cytolib,CytoML,DeepBlueR,DelayedArray,DelayedDataFrame,DelayedMatrixStats,DEP,DepecheR,diffloop,doseR,esetVis,ExperimentSubset,FindMyFriends,flowDensity,flowPlots,flowSpecs,flowWorkspace,FunciSNP,GA4GHclient,GDSArray,GeneAnswers,GenomeInfoDb,GenomicInteractions,GenomicRanges,GenomicTuples,genoset,GenVisR,GOexpress,HCAMatrixBrowser,HDF5Array,ILoReg,ImmuneSpaceR,InteractionSet,interactiveDisplay,interactiveDisplayBase,ipdDb,IRanges,KEGGlincs,LoomExperiment,MACSQuantifyR,maftools,matter,Modstrings,monocle,MultiAssayExperiment,MultiBaC,MultiDataSet,nearBynding,OMICsPCA,Omixer,OmnipathR,openCyto,oposSOM,OSAT,phantasus,phemd,PhyloProfile,pipeComp,plethy,plyranges,psygenet2r,R453Plus1Toolbox,R4RNA,RaggedExperiment,rBiopaxParser,Rcpi,RedeR,ReportingTools,ResidualMatrix,rexposome,RImmPort,RTCGA,S4Vectors,SC3,scater,scmap,SeqArray,SingleCellExperiment,Spaniel,sparseMatrixStats,SpatialExperiment,spatialHeatmap,SplicingGraphs,SQLDataFrame,Structstrings,Sushi,TileDBArray,TreeAndLeaf,treeio,TreeSummarizedExperiment,TVTB,Ularcirc,VariantExperiment,VCFArray,VennDetail,weitrix,XVector,zellkonverter", "id": "DataRepresentation" }, "children": [ ] }, { "data": "GUI (54)", "attr": { "packageList": "adductomicsR,affylmGUI,AnnotationHub,bioCancer,canceR,CrossICC,crossmeta,DiscoRhythm,epivizr,epivizrChart,epivizrStandalone,ExperimentHub,ExperimentHubData,explorase,flowcatchR,flowPloidy,GA4GHshiny,GEM,GeneTonic,GmicR,GSCA,ideal,interactiveDisplay,interactiveDisplayBase,iSEE,iSEEu,IsoCorrectoRGUI,IsoGeneGUI,limmaGUI,MACSQuantifyR,mcaGUI,metavizr,MethylAid,MSGFgui,MSstatsQCgui,omicplotR,OMICsPCA,oneSENSE,PanVizGenerator,pcaExplorer,phantasus,plotGrouper,pRolocGUI,Prostar,psichomics,rTRMui,sangeranalyseR,SC3,statTarget,TCGAbiolinksGUI,TSCAN,TVTB,uSORT,wpm", "id": "GUI" }, "children": [ ] }, { "data": "ThirdPartyClient (29)", "attr": { "packageList": "adductomicsR,AnnotationHub,BiocDockerManager,brendaDb,BrowserViz,cBioPortalData,DeepBlueR,ExperimentHub,ExperimentHubData,GA4GHclient,gaggle,graphite,igvR,ImmuneSpaceR,KEGGlincs,KEGGREST,lpsymphony,maigesPack,ncRNAtools,OmnipathR,PSICQUIC,RCy3,RCyjs,rfaRm,RGraph2js,rpx,rWikiPathways,sevenbridges,slinky", "id": "ThirdPartyClient" }, "children": [ ] } ] }, { "data": "ResearchField (903)", "attr": { "packageList": "cbaf,iGC,INDEED,MethTargetedNGS,MetID,PhosR,RankProd,rDGIdb,SCANVIS,sRACIPE", "id": "ResearchField" }, "children": [ { "childnum": 0, "data": "Agroinformatics", "children": [ ] }, { "data": "BiomedicalInformatics (62)", "attr": { "packageList": "artMS,ASAFE,CancerInSilico,cbaf,cellTree,ChemmineOB,ChemmineR,coRdon,dearseq,deco,decompTumor2Sig,edgeR,eiR,flowAI,fmcsR,frenchFISH,GAprediction,gCrisprTools,GeneAccord,geneClassifiers,GenomicOZone,gwasurvivr,hummingbird,ISAnalytics,IsoformSwitchAnalyzeR,LACE,limma,mdp,MEAT,messina,metaseqR2,miRSM,miRspongeR,MOGAMUN,MouseFM,netboost,netDx,OMICsPCA,OncoScore,oppti,OPWeight,Pigengene,powerTCR,psichomics,psygenet2r,PubScore,RandomWalkRestartMH,randRotation,Rcpi,rexposome,RImmPort,RIVER,rmelting,rScudo,SigsPack,sincell,SparseSignatures,ssPATHS,STROMA4,timescape,TRONCO,VERSO", "id": "BiomedicalInformatics" }, "children": [ ] }, { "childnum": 0, "data": "Biophysics", "children": [ ] }, { "data": "CellBiology (54)", "attr": { "packageList": "BASiCS,CancerInSilico,CellNOptR,cellTree,CFAssay,cn.mops,CNORdt,CNORfeeder,CNORode,CONFESS,CRImage,CytoDx,CytoTree,dearseq,debCAM,destiny,dexus,diffcyt,edgeR,fastLiquidAssociation,FISHalyseR,flowcatchR,flowDensity,flowMeans,FlowSOM,flowSpy,frenchFISH,GateFinder,gCrisprTools,GenomicOZone,GRmetrics,HPAanalyze,hpar,idpr,ImpulseDE2,KEGGlincs,limma,LineagePulse,LiquidAssociation,MetaCyto,metaseqR2,MPRAnalyze,netresponse,OVESEG,panelcn.mops,pathwayPCA,Prize,SamSPECTRAL,sincell,spatialHeatmap,staRank,ternarynet,tRanslatome,uSORT", "id": "CellBiology" }, "children": [ ] }, { "data": "Cheminformatics (13)", "attr": { "packageList": "AlpsNMR,ASICS,BridgeDbR,ChemmineOB,ChemmineR,customCMPdb,eiR,fmcsR,limma,MWASTools,rcellminer,Rcpi,rmelting", "id": "Cheminformatics" }, "children": [ ] }, { "data": "ComparativeGenomics (8)", "attr": { "packageList": "AssessORF,cbaf,FindMyFriends,InterMineR,OmaDB,PanVizGenerator,phemd,SynExtend", "id": "ComparativeGenomics" }, "children": [ ] }, { "childnum": 0, "data": "ComputationalChemistry", "children": [ ] }, { "data": "Epigenetics (63)", "attr": { "packageList": "AlphaBeta,ALPS,BEAT,BiFET,BPRMeth,bumphunter,cbaf,Chicago,chipenrich,ChIPSeqSpike,ChromSCape,chromswitch,cicero,COCOA,COHCAP,compartmap,DeepBlueR,DEScan2,DiffBind,DMRcate,dmrseq,edgeR,ENmix,EpiDISH,epihet,GAprediction,GenoGAM,GOTHiC,idr2d,InTAD,ISoLDE,limma,mCSEA,MEAT,Melissa,metaseqR2,methimpute,methInheritSim,MethPed,MethReg,methylInheritance,methylSig,minfi,MIRA,mitch,msgbsR,netboost,nuCpos,omicRexposome,OMICsPCA,omicsPrint,pathwayPCA,proActiv,PubScore,recountmethylation,REMP,rnaEditr,RnBeads,sevenC,srnadiff,TCseq,TOAST,variancePartition", "id": "Epigenetics" }, "children": [ ] }, { "data": "Epitranscriptomics (1)", "attr": { "packageList": "EpiTxDb", "id": "Epitranscriptomics" }, "children": [ ] }, { "data": "FunctionalGenomics (53)", "attr": { "packageList": "AlphaBeta,annotatr,BasicSTARRseq,CAGEr,cellTree,chipenrich,chromPlot,chromswitch,COCOA,coMET,customProDB,DEComplexDisease,DEWSeq,DiffBind,dmrseq,edgeR,EGAD,eisaR,FGNet,gCrisprTools,GeneAccord,GenomicOZone,heatmaps,idr2d,InterMineR,IsoformSwitchAnalyzeR,limma,loci2path,LOLA,maftools,MAGeCKFlute,metaseqR2,MIRA,MOMA,MouseFM,mpra,ncRNAtools,normr,OmaDB,OMICsPCA,ORFik,pathwayPCA,preciseTAD,proActiv,rDGIdb,rfaRm,RITAN,RIVER,sevenC,sincell,TSRchitect,tximeta,variancePartition", "id": "FunctionalGenomics" }, "children": [ ] }, { "data": "Genetics (200)", "attr": { "packageList": "aCGH,adaptest,AGDEX,AllelicImbalance,AlphaBeta,ASAFE,AssessORF,BANDITS,BaseSpaceR,BEAT,BiFET,BioMM,biomvRCNS,Biostrings,BiSeq,BPRMeth,BSgenome,BUMHMM,calm,CancerMutationAnalysis,CAnD,cbaf,CexoR,ChIPComp,chromPlot,CINdex,cleanUpdTSeq,Clomial,cn.mops,coMET,compartmap,consensusSeekeR,contiBAIT,copynumber,cpvSNP,CSAR,csaw,ctsGE,DBChIP,dearseq,DECIPHER,decompTumor2Sig,deepSNV,diffuStats,discordant,distinct,DMRcate,dpeak,DRIMSeq,easyRNASeq,edgeR,EGSEA,ensembldb,erccdashboard,exomeCopy,FamAgg,fastLiquidAssociation,fCCAC,FRASER,frenchFISH,FRGEpistasis,gage,gCrisprTools,GeneAccord,GeneBreak,GeneGeneInteR,geneplast,geneRxCluster,GENESIS,GeneticsDesign,GeneticsPed,geneXtendeR,genoCN,GenoGAM,GenomeInfoDb,genomeIntervals,genomes,GenomicAlignments,GenomicFeatures,GenomicFiles,GenomicOZone,GenomicRanges,GenomicScores,genotypeeval,genphen,GenRank,GEWIST,GGBase,GGPA,GGtools,GPA,gwascat,gwasurvivr,hapFabia,HDTD,HIBAG,HybridMTest,iGC,IgGeneUsage,Imetagene,infercnv,intansv,interactiveDisplay,interactiveDisplayBase,ISoLDE,KnowSeq,limma,Linnorm,LiquidAssociation,loci2path,logicFS,martini,MassArray,MatrixRider,mCSEA,MEDIPS,Melissa,metaCCA,metagene,metagene2,MethTargetedNGS,MGFM,MGFR,MLP,mosaics,MouseFM,muscle,MutationalPatterns,NarrowPeaks,netresponse,normr,nucleoSim,nucleR,nuCpos,NuPoP,OmaDB,omicsPrint,OUTRIDER,packFinder,panelcn.mops,pathview,pathwayPCA,PCAN,Pi,podkat,PREDA,primirTSS,psygenet2r,PubScore,QDNAseq,qpgraph,QSutils,Qtlizer,QuasR,rain,randRotation,Rcade,RCASPAR,regioneR,Rgin,riboSeqR,RIVER,RNASeqR,rRDP,RRHO,Rsubread,rSWeeP,RVS,SAIGEgds,sangeranalyseR,SBGNview,scoreInvHap,semisup,SeqArray,seqCNA,SeqVarTools,similaRpeak,SLGI,SNPRelate,SplicingGraphs,sscu,ssviz,StructuralVariantAnnotation,SummarizedExperiment,Sushi,SynExtend,systemPipeR,TCGAbiolinksGUI,TEQC,TIN,TitanCNA,transite,traseR,trigger,trio,TVTB,Ularcirc,VariantAnnotation,VariantFiltering,VariantTools", "id": "Genetics" }, "children": [ ] }, { "data": "ImmunoOncology (449)", "attr": { "packageList": "AIMS,ALDEx2,amplican,Anaquin,AneuFinder,anota2seq,apComplex,apeglm,ArrayExpressHTS,artMS,ASpli,ATACseqQC,attract,bacon,BADER,ballgown,bambu,banocc,Basic4Cseq,BASiCS,BatchQC,BayesSpace,bayNorm,bcSeq,BDMMAcorrect,BEARscc,BEAT,BiFET,bioassayR,BiocOncoTK,biomformat,BioNetStat,biotmle,BitSeq,bluster,BPRMeth,BRAIN,BUMHMM,bumphunter,calm,CAMERA,CancerInSilico,caOmicsV,Cardinal,casper,CATALYST,CausalR,ccfindR,ccrepe,CellaRepertorium,cellHTS2,cellity,CellNOptR,CellTrails,cellTree,CEMiTool,CeTF,CFAssay,chipenrich,ChIPSeqSpike,chromstaR,chromswitch,chromVAR,cicero,Clomial,CNORdt,CNORode,COCOA,CODEX,CoGAPS,compartmap,COMPASS,compcodeR,CONFESS,contiBAIT,CopywriteR,coRdon,coseq,cosmiq,CountClust,countsimQC,covEB,CoverageView,cqn,CRISPRseek,CrispRVariants,ctgGEM,cTRAP,ctsGE,customProDB,cydar,CytoDx,cytolib,cytomapper,CytoML,dada2,DaMiRseq,dcGSA,dearseq,debrowser,DECIPHER,decontam,DeepBlueR,DEFormats,DegNorm,DEGreport,DEGseq,DEP,DepecheR,DEqMS,derfinder,derfinderHelper,derfinderPlot,DEScan2,DESeq,DESeq2,DEsingle,DEsubs,DEXSeq,dexus,diffcoexp,diffcyt,DirichletMultinomial,discordant,dmrseq,doppelgangR,DRIMSeq,DropletUtils,dupRadar,easyRNASeq,EBSeq,EBSeqHMM,EDASeq,EDDA,edgeR,eegc,EGSEA,ELBOW,EnhancedVolcano,ENmix,EnrichmentBrowser,EpiDISH,erccdashboard,ERSSA,esATAC,EventPointer,ExCluster,exomePeak2,FCBF,fcoex,flagme,flowAI,flowBeads,flowBin,flowCHIC,flowCL,flowClean,flowClust,flowCore,flowCyBar,flowFit,flowMap,flowMatch,flowMeans,flowMerge,flowPeaks,flowPlots,FlowRepositoryR,flowSpecs,flowStats,flowTime,flowTrans,flowType,flowUtils,flowViz,flowVS,flowWorkspace,gaga,GAprediction,GateFinder,gCrisprTools,GDCRNATools,GeneStructureTools,GenoGAM,GenomicAlignments,gespeR,ggcyto,GmicR,GOexpress,goseq,goSTAG,GOTHiC,GRmetrics,GRridge,GSEABenchmarkeR,GUIDEseq,HDF5Array,HTSFilter,iASeq,iasva,icetea,iCNV,ideal,IHW,imageHTS,IMAS,immunoClust,ImpulseDE2,INDEED,InPAS,InTAD,IntEREst,IPO,iSEE,iSEEu,isobar,IsoCorrectoR,IsoCorrectoRGUI,IsoformSwitchAnalyzeR,ISoLDE,isomiRs,IVAS,JunctionSeq,KnowSeq,limma,LineagePulse,Linnorm,LOBSTAHS,LoomExperiment,M3C,MAIT,MassArray,MassSpecWavelet,MCbiclust,mCSEA,Melissa,Metab,metabomxtr,MetaCyto,metagenomeFeatures,metagenomeSeq,metaMS,MetaNeighbor,metaSeq,metaseqR,metaseqR2,metavizr,MetCirc,methimpute,methInheritSim,MethPed,methylInheritance,MetNet,mfa,MGFR,microbiomeExplorer,MIMOSA,minfi,MIRA,MiRaGE,mixOmics,MLSeq,monocle,MPRAnalyze,msgbsR,MSGFgui,MSGFplus,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,MSstatsTMT,MSstatsTMTPTM,muscat,mzID,mzR,NBSplice,ncdfFlow,netprioR,NOISeq,nuCpos,omicplotR,omicRexposome,OMICsPCA,omicsPrint,oneSENSE,openCyto,OPWeight,ORFik,Oscope,OUTRIDER,PAIRADISE,PANR,PathoStat,PathwaySplice,pcaExplorer,pepXMLTab,perturbatr,PGA,pgca,phantasus,phenopath,philr,phyloseq,Pigengene,plgem,plotGrouper,pogos,Polyfit,prada,prebs,primirTSS,Prize,proBAMr,PROcess,pRoloc,PROPER,Prostar,ProteoMM,psichomics,PureCN,qcmetrics,qPLEXanalyzer,QuasR,qusage,Rcwl,RcwlPipelines,Rdisop,recount,recoup,regionReport,regsplice,ReportingTools,RGMQL,rgsepd,RMassBank,RNAdecay,RNAinteract,RNAither,rnaSeqMap,RNASeqPower,RNASeqR,RnaSeqSampleSize,RnBeads,rols,ropls,ROTS,rpx,rRDP,Rsubread,rTANDEM,RTCA,RTCGA,RUVSeq,RVS,samExploreR,sampleClassifier,SamSPECTRAL,sapFinder,SC3,SCAN.UPC,scater,scDataviz,scDD,scde,scFeatureFilter,scmap,scmeth,SCnorm,scone,Sconify,scPipe,scran,scRepertoire,scruff,scuttle,SDAMS,SeqGSEA,seqplots,SGSeq,shinyTANDEM,SIAMCAT,SigFuge,sights,SIMAT,SIMD,SIMLR,sincell,SingleCellExperiment,singleCellTK,slalom,SMITE,sparseDOSSA,sparsenetgls,SpatialDecon,SpatialExperiment,splatter,SplicingGraphs,SPLINTER,srnadiff,sSeq,SSPA,ssviz,STAN,staRank,statTarget,strandCheckR,STROMA4,subSeq,sva,SVAPLSseq,SWATH2stats,switchde,synapter,synlet,systemPipeR,TargetSearch,TCC,tenXplore,TFEA.ChIP,timeOmics,TimeSeriesExperiment,TitanCNA,tofsims,ToPASeq,topdownr,TPP,transcriptogramer,transcriptR,TransView,Trendy,TRONCO,tweeDEseq,tximeta,tximport,Uniquorn,uSORT,variancePartition,vasp,VaSP,vidger,wavClusteR,wiggleplotr,XBSeq,xcms,yamss,zFPKM,zinbwave", "id": "ImmunoOncology" }, "children": [ ] }, { "data": "Lipidomics (11)", "attr": { "packageList": "biosigner,Cardinal,lipidr,LOBSTAHS,MWASTools,OmicsLonDA,pathwayPCA,proFIA,RankProd,ropls,statTarget", "id": "Lipidomics" }, "children": [ ] }, { "data": "MathematicalBiology (8)", "attr": { "packageList": "AlphaBeta,CancerInSilico,GeneAccord,ISoLDE,missRows,MouseFM,RandomWalkRestartMH,sRACIPE", "id": "MathematicalBiology" }, "children": [ ] }, { "data": "Metabolomics (75)", "attr": { "packageList": "adductomicsR,AlpsNMR,ASICS,Autotuner,BiGGR,bioassayR,BioNetStat,biosigner,BridgeDbR,calm,CAMERA,ChemmineOB,ChemmineR,cliqueMS,CluMSID,combi,cosmiq,DIAlignR,diffuStats,EGSEA,eiR,FELLA,fmcsR,graphite,hmdbQuery,INDEED,IPO,IsoCorrectoR,IsoCorrectoRGUI,limma,LOBSTAHS,MAIT,marr,Metab,metabCombiner,metabolomicsWorkbenchR,metabomxtr,metaMS,MetCirc,MetNet,mixOmics,MsCoreUtils,MSPrep,msPurity,MWASTools,mzR,ncGTW,netboost,NormalyzerDE,OmicsLonDA,OmicsMarkeR,pathview,pathwayPCA,peakPantheR,PepsNMR,pmp,POMA,proFIA,QFeatures,RankProd,Rdisop,RMassBank,ropls,rWikiPathways,SBGNview,SDAMS,SIMAT,sparsenetgls,Spectra,statTarget,structToolbox,timeOmics,tofsims,xcms,yamss", "id": "Metabolomics" }, "children": [ ] }, { "data": "Metagenomics (28)", "attr": { "packageList": "ALDEx2,animalcules,banocc,biomformat,ccrepe,combi,coRdon,dada2,decontam,DirichletMultinomial,Maaslin2,metagenomeFeatures,metagenomeSeq,metavizr,microbiome,microbiomeExplorer,mixOmics,MMUPHin,omicplotR,PathoStat,PERFect,philr,phyloseq,RCM,reconsi,SIAMCAT,sparseDOSSA,timeOmics", "id": "Metagenomics" }, "children": [ ] }, { "data": "Pharmacogenetics (11)", "attr": { "packageList": "ChemmineOB,ChemmineR,eiR,fmcsR,gCrisprTools,PharmacoGx,RadioGx,rcellminer,rDGIdb,ToxicoGx,Xeva", "id": "Pharmacogenetics" }, "children": [ ] }, { "data": "Pharmacogenomics (14)", "attr": { "packageList": "ChemmineOB,ChemmineR,CoreGx,eiR,fmcsR,gCrisprTools,gwasurvivr,PharmacoGx,pogos,RadioGx,rcellminer,rDGIdb,ToxicoGx,Xeva", "id": "Pharmacogenomics" }, "children": [ ] }, { "data": "Phylogenetics (4)", "attr": { "packageList": "ggtree,ggtreeExtra,sitePath,treeio", "id": "Phylogenetics" }, "children": [ ] }, { "data": "Proteomics (145)", "attr": { "packageList": "artMS,ASEB,AssessORF,bioassayR,biobroom,BioNetStat,biosigner,BRAIN,calm,Cardinal,CausalR,CellNOptR,ChemmineOB,ChemmineR,cisPath,cleaver,clippda,CNORdt,CNORfeeder,CNORode,customProDB,cydar,DAPAR,deco,deltaGseg,DEP,DEqMS,DIAlignR,diffcyt,diffuStats,DominoEffect,Doscheda,drawProteins,EGSEA,eiR,fCI,fmcsR,GraphPAC,HPAanalyze,hpar,idpr,IMMAN,infinityFlow,InterMineR,iPAC,isobar,KinSwingR,limma,LPEadj,MassSpecWavelet,MBQN,mitch,mixOmics,MsCoreUtils,MSGFgui,MSGFplus,msImpute,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,MSstatsConvert,MSstatsPTM,MSstatsQC,MSstatsQCgui,MSstatsSampleSize,MSstatsTMT,MSstatsTMTPTM,mzID,mzR,NormalyzerDE,NPARC,omicRexposome,OmicsLonDA,oppti,PAA,Path2PPI,pathview,pathwayPCA,PCpheno,PECA,pepXMLTab,PGA,pgca,phemd,phosphonormalizer,plgem,PLPE,POMA,ppiStats,PrInCE,proBAMr,proBatch,PROcess,procoil,proDA,proFIA,pRoloc,pRolocGUI,Prostar,ProteomicsAnnotationHubData,ProteoMM,ProtGenerics,pulsedSilac,Pviz,qcmetrics,QFeatures,qPLEXanalyzer,QuartPAC,rain,RankProd,RCASPAR,Rcpi,ReactomeGSA,ropls,ROTS,RpsiXML,rpx,rScudo,rTANDEM,Rtpca,sapFinder,SBGNview,ScISI,scp,SDAMS,shinyTANDEM,SLGI,SMAD,SpacePAC,sparsenetgls,specL,Spectra,statTarget,SubCellBarCode,SWATH2stats,synapter,timeOmics,tofsims,topdownr,TPP,TPP2D,wpm,XINA", "id": "Proteomics" }, "children": [ ] }, { "childnum": 0, "data": "StructuralGenomics", "children": [ ] }, { "data": "StructuralPrediction (6)", "attr": { "packageList": "BUMHMM,circRNAprofiler,DNAshapeR,idpr,ncRNAtools,nearBynding", "id": "StructuralPrediction" }, "children": [ ] }, { "data": "SystemsBiology (82)", "attr": { "packageList": "artMS,BioCor,BioNetStat,CancerInSilico,CausalR,cellTree,ceRNAnetsim,CHRONOS,COCOA,coexnet,cogena,CoRegFlux,CoRegNet,dearseq,DeMAND,DEsubs,diggit,doseR,edgeR,EGAD,EGSEA,epiNEM,gage,gCrisprTools,GeneAccord,geneplast,GENIE3,GenomicOZone,GmicR,IMMAN,INSPEcT,InterMineR,IsoformSwitchAnalyzeR,KnowSeq,limma,LOLA,mdp,MEIGOR,metaseqR2,microbiome,MIRA,mnem,MOGAMUN,MOMA,MouseFM,multiOmicsViz,MWASTools,netboxr,netDx,OmnipathR,oppar,Path2PPI,pathview,pathwayPCA,paxtoolsr,PhosR,Pigengene,pmm,PrInCE,progeny,PubScore,pwOmics,rain,RandomWalkRestartMH,RankProd,rcellminer,Rcpi,ReactomeGSA,regutools,RIVER,rScudo,rsemmed,SBGNview,sincell,SMITE,SPONGE,sRACIPE,transcriptogramer,trena,viper,vulcan,XINA", "id": "SystemsBiology" }, "children": [ ] }, { "data": "Transcriptomics (137)", "attr": { "packageList": "ADImpute,aggregateBioVar,ALDEx2,AUCell,bacon,bambu,BASiCS,batchelor,BayesSpace,BEARscc,biosigner,blacksheepr,bluster,brainflowprobes,BUMHMM,CAGEfightR,calm,CARNIVAL,CausalR,cbaf,ccfindR,CellaRepertorium,cellity,CellMixS,CEMiTool,ceRNAnetsim,consensusDE,consensusOV,cTRAP,dasper,dearseq,deco,DepecheR,DEsingle,diffuStats,dittoSeq,DropletUtils,Dune,edgeR,eisaR,fcoex,GeneStructureTools,GeneTonic,GenomicOZone,getDEE2,globalSeq,GWENA,HumanTranscriptomeCompendium,icetea,ILoReg,infercnv,iSEE,iSEEu,IsoformSwitchAnalyzeR,kissDE,KnowSeq,limma,M3Drop,made4,maser,MAST,mbkmeans,mdp,megadepth,MetaNeighbor,metaseqR2,MetaVolcanoR,mitch,MOGAMUN,MOMA,netboost,netSmooth,NewWave,omicplotR,omicRexposome,OmicsLonDA,omicsPrint,OUTRIDER,pathwayPCA,peco,phantasus,phemd,Pigengene,pipeComp,proActiv,psichomics,RCAS,RcisTarget,ReactomeGSA,RegEnrich,restfulSE,RIVER,RNAdecay,ropls,rScudo,sarks,SC3,scAlign,SCANVIS,scater,scBFA,scCB2,scds,scHOT,scMAGeCK,scmap,scMerge,scone,scran,scRecover,scry,scuttle,SeqGate,SingleR,slalom,slingshot,Spaniel,SpatialCPie,SpatialDecon,splatter,SPONGE,ssPATHS,switchde,tenXplore,TFEA.ChIP,TFutils,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,tomoda,topconfects,tradeSeq,tximeta,tximport,variancePartition,weitrix,zinbwave", "id": "Transcriptomics" }, "children": [ ] } ] }, { "data": "StatisticalMethod (727)", "attr": { "packageList": "AMARETTO,ArrayTools,AWFisher,bacon,ballgown,BANDITS,BEclear,BioCor,BiocSklearn,BioQC,BUScorrect,CAnD,CATALYST,ClusterJudge,ClusterSignificance,CountClust,covEB,cpvSNP,CytoDx,dcGSA,decompTumor2Sig,deltaCaptureC,DeMAND,DeMixT,discordant,distinct,divergence,EBSeq,EBSeqHMM,EmpiricalBrownsMethod,fabia,FunChIP,garfield,GENESIS,GGPA,GISPA,glmSparseNet,GPA,GSAR,gscreend,gsean,Harman,HDTD,HIBAG,HiLDA,iasva,iCARE,ImpulseDE,ImpulseDE2,INDEED,infercnv,IntramiRExploreR,IsoformSwitchAnalyzeR,iterClust,iteremoval,IWTomics,joda,lefser,LineagePulse,MACPET,MCbiclust,MDTS,MeasurementError.cor,metaCCA,MetaCyto,methInheritSim,methylInheritance,MethylMix,MetID,missRows,mogsa,MPRAnalyze,Mulcom,MultiBaC,MultiMed,muscat,NBSplice,NeighborNet,netboost,netReg,npGSEA,nucleoSim,omicRexposome,onlineFDR,OpenStats,Oscope,padma,pageRank,PAIRADISE,pandaR,peco,PhenStat,phosphonormalizer,PING,plotGrouper,PoTRA,PPInfer,profileScoreDist,QUBIC,randPack,randRotation,RankProd,Rariant,receptLoss,RGSEA,RJMCMCNucleosomes,ROCpAI,rqt,rSWeeP,Rtreemix,RUVnormalize,safe,SAIGEgds,scde,selectKSigs,signeR,SNPRelate,SomaticSignatures,SRGnet,srnadiff,SSPA,stageR,STATegRa,survtype,sva,swfdr,switchBox,synergyfinder,target,TCGAbiolinksGUI,TFARM,TitanCNA,TMixClust,tweeDEseq,Uniquorn,vasp,VaSP,waddR,XCIR,YAPSA", "id": "StatisticalMethod" }, "children": [ { "data": "Bayesian (70)", "attr": { "packageList": "affylmGUI,ALDEx2,AMARETTO,apeglm,ASSIGN,BaalChIP,bacon,BAGS,BANDITS,banocc,BASiCS,BayesKnockdown,BDMMAcorrect,BitSeq,BPRMeth,BUMHMM,BUScorrect,calm,ccfindR,celda,Clomial,CoGAPS,covEB,CSSP,ctsGE,deco,DEqMS,DESeq2,DMCFB,EBcoexpress,EBSeqHMM,edgeR,gemini,genphen,GmicR,graper,GRENITS,GRridge,HiLDA,hummingbird,IgGeneUsage,infercnv,limma,limmaGUI,Logolas,MADSEQ,Melissa,metaseqR2,mfa,MOFA,MOFA2,networkBMA,NormalyzerDE,normr,omicplotR,OpenStats,pcaMethods,phenopath,proDA,PROPS,puma,R3CPET,RIVER,RJMCMCNucleosomes,scDD,scde,sparseDOSSA,tigre,TRONCO,wavClusteR", "id": "Bayesian" }, "children": [ ] }, { "data": "Classification (145)", "attr": { "packageList": "a4Classif,a4Core,AIMS,AlpsNMR,antiProfiles,BadRegionFinder,BiocNeighbors,bioDist,BioMM,BioSeqClass,biosigner,BUMHMM,cancerclass,Cardinal,CHETAH,ChromSCape,ClassifyR,Clonality,clst,clstutils,ClusterSignificance,CMA,CNVPanelizer,cola,CONFESS,consensusOV,CoreGx,COSNet,CRImage,CrossICC,ctc,CytoDx,dada2,DaMiRseq,decontam,DeMixT,DepecheR,dexus,DirichletMultinomial,dualKS,EGSEA,eisa,epigenomix,escape,evaluomeR,ExpressionView,fastseg,FCBF,flowcatchR,gaga,GARS,geneClassifiers,genefu,geNetClassifier,genphen,GenVisR,GGPA,glmSparseNet,GPA,gpls,graper,GRridge,GSgalgoR,iCOBRA,idr2d,interactiveDisplay,interactiveDisplayBase,iterativeBMA,kebabs,KnowSeq,LedPred,lefser,LinkHD,logicFS,MACPET,made4,maftools,maigesPack,maPredictDSC,massiR,MEB,messina,metagenomeSeq,MethPed,methVisual,microbiomeExplorer,MiPP,miRNAtap,mixOmics,MLInterfaces,MLSeq,MSstatsSampleSize,netDx,NetPathMiner,normr,NuPoP,omicade4,OmicsMarkeR,PAA,pathwayPCA,peco,PERFect,PharmacoGx,phenoTest,phyloseq,Pigengene,preciseTAD,procoil,pRoloc,PROPS,RadioGx,RBioinf,rexposome,rfPred,RGSEA,Rmagpie,ROCpAI,ropls,rRDP,rScudo,sampleClassifier,SC3,scClassify,scds,SCFA,scmap,scRepertoire,SemDist,semisup,sevenC,SIAMCAT,SigCheck,sigFeature,SingleCellSignalR,SingleR,ssPATHS,STROMA4,SubCellBarCode,switchBox,timeOmics,TNBC.CMS,TTMap,twoddpcr,vbmp,Xeva", "id": "Classification" }, "children": [ ] }, { "data": "Clustering (249)", "attr": { "packageList": "adSplit,AMARETTO,ANF,artMS,BayesSpace,BEARscc,BHC,BicARE,bigPint,BiocNeighbors,BioCor,bioDist,bluster,BPRMeth,BUScorrect,CAGEr,CancerSubtypes,Cardinal,CATALYST,ccfindR,celda,CellaRepertorium,CellTrails,cellTree,CGEN,CHARGE,ChemmineOB,ChemmineR,CHETAH,ChromSCape,chromswitch,cicero,Clomial,CluMSID,clustComp,clusterExperiment,ClusterJudge,clusterProfiler,clusterSeq,ClusterSignificance,clusterStab,CoGAPS,cogena,cola,CONFESS,ConsensusClusterPlus,consensusDE,consensusOV,CORREP,CountClust,CrossICC,ctc,ctgGEM,ctsGE,cummeRbund,cytofast,CytoTree,ddPCRclust,debrowser,DECIPHER,deco,DEComplexDisease,deltaGseg,DepecheR,DESeq2,destiny,diffcyt,diffHic,DirichletMultinomial,DrugVsDisease,Dune,EBarrays,edgeR,eiR,evaluomeR,fabia,fcScan,FGNet,FindMyFriends,flowCHIC,flowClust,flowCyBar,flowDensity,flowFP,flowMatch,flowMeans,flowMerge,flowPeaks,FlowSOM,flowSpy,fmcsR,FunChIP,GARS,GateFinder,genefu,geneRecommender,geneRxCluster,GenomicOZone,GGPA,ggtree,GmicR,GOexpress,GOpro,GOSemSim,GOSim,goSTAG,GOsummaries,GPA,gpart,GraphPAC,GSEAmining,GSgalgoR,GWENA,hapFabia,hierGWAS,hierinf,HIPPO,hopach,iBBiG,iClusterPlus,ILoReg,immunoClust,iPAC,iSEE,iSEEu,isomiRs,iterClust,kebabs,LEA,limma,Linnorm,M3C,maanova,MACPET,made4,maigesPack,MantelCorr,massiR,mbkmeans,mcaGUI,MCbiclust,Melissa,meshes,MetaCyto,metagenomeSeq,metaseqR2,methVisual,methyvim,Mfuzz,microbiomeExplorer,miRSM,Mirsynergy,MLInterfaces,MLSeq,MmPalateMiRNA,MOGAMUN,mogsa,MOMA,monocle,multiClust,nearBynding,netboost,nethet,NetPathMiner,netresponse,netSmooth,omicade4,OMICsPCA,Onassis,PANR,phantasus,phemd,phenoTest,phyloseq,PICS,Pigengene,PING,pipeComp,PloGO2,powerTCR,preciseTAD,pRoloc,puma,QuartPAC,QUBIC,RBioinf,RDRToolbox,rexposome,RIVER,RNASeqR,rqubic,rrvgo,rScudo,runibic,SAGx,SamSPECTRAL,SC3,scCB2,scDD,SCFA,scGPS,scran,selectKSigs,semisup,SIAMCAT,SigFuge,SIMLR,simplifyEnrichment,sincell,SingleCellSignalR,singleCellTK,SingleR,slingshot,SomaticSignatures,SpacePAC,Spaniel,SpatialCPie,spatialHeatmap,SpeCond,SpectralTAD,STATegRa,supraHex,survtype,SynExtend,systemPipeShiny,TADCompare,TCseq,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,timeOmics,TimeSeriesExperiment,TimiRGeN,TMixClust,TNBC.CMS,tomoda,tradeSeq,transcriptogramer,TransView,treeio,TRONCO,tscR,TSRchitect,TTMap,vasp,VaSP,ViSEAGO,YAPSA,yarn", "id": "Clustering" }, "children": [ ] }, { "data": "DecisionTree (7)", "attr": { "packageList": "CMA,DEGraph,flowUtils,GENIE3,Pigengene,ScISI,TargetSearch", "id": "DecisionTree" }, "children": [ ] }, { "data": "DimensionReduction (55)", "attr": { "packageList": "adaptest,AffiXcan,BiocSingular,BiocSklearn,cellity,CellTrails,CoGAPS,combi,corral,densvis,DepecheR,esetVis,fmrs,gcatest,GENESIS,gep2pep,glmSparseNet,globalSeq,ILoReg,iSEE,iSEEu,lfa,M3Drop,made4,missRows,MOFA,MOFA2,Nebulosa,netboost,netSmooth,OMICsPCA,oneSENSE,pathwayPCA,pcaExplorer,phemd,Pigengene,RCM,RDRToolbox,rnaEditr,SC3,scAlign,scater,scBFA,schex,scry,scTensor,scTGIF,slalom,snifter,ssPATHS,STATegRa,tenXplore,timeOmics,weitrix,zinbwave", "id": "DimensionReduction" }, "children": [ ] }, { "data": "FeatureExtraction (47)", "attr": { "packageList": "bambu,biosigner,BPRMeth,BUMHMM,BUScorrect,CrossICC,deco,DepecheR,diffcyt,evaluomeR,FCBF,GARS,GeneAccord,genphen,HIREewas,iasva,iSEE,iSEEu,KnowSeq,M3Drop,maftools,mAPKL,martini,Melissa,MicrobiotaProcess,MOMA,multiClust,netReg,OmicsMarkeR,pathwayPCA,preciseTAD,rCGH,Rcpi,RDRToolbox,Rgin,rnaEditr,rScudo,sarks,SIAMCAT,sigFeature,SpatialDecon,SpectralTAD,synlet,TADCompare,timeOmics,trena,zFPKM", "id": "FeatureExtraction" }, "children": [ ] }, { "data": "GraphAndNetwork (132)", "attr": { "packageList": "ANF,apComplex,ASpediaFI,BatchQC,BiGGR,biocGraph,BioMVCClass,BioNet,BioNetStat,CausalR,cellTree,CEMiTool,ceRNAnetsim,CHRONOS,coexnet,CoRegNet,CORREP,COSNet,DART,dcanr,DEGraph,DEsubs,diffuStats,EGAD,EGSEA,EnrichmentBrowser,enrichTF,fcoex,FELLA,FindMyFriends,gaggle,GeneNetworkBuilder,GENIE3,glmSparseNet,GmicR,goProfiles,GOstats,gramm4R,graph,GraphAlignment,GraphAT,graphite,GRENITS,GRridge,GSEABase,GSEABenchmarkeR,gsean,GWENA,hipathia,hyperdraw,hypergraph,ibh,IMMAN,joda,KEGGgraph,KEGGlincs,keggorthology,maigesPack,martini,MetaboSignal,minet,mirIntegrator,MOGAMUN,MVCClass,NCIgraph,NeighborNet,netbenchmark,netbiov,netboost,netboxr,nethet,NetPathMiner,netReg,netresponse,netSmooth,OmnipathR,paircompviz,pandaR,PANR,PathoStat,pathRender,pathview,PathwaySplice,paxtoolsr,PCpheno,Pi,Pigengene,pkgDepTools,plotGrouper,PoTRA,PPInfer,ppiStats,predictionet,PSICQUIC,qpgraph,QuaternaryProd,R3CPET,RandomWalkRestartMH,RBGL,RCy3,RCyjs,RDAVIDWebService,RedeR,Rgin,RGraph2js,Rgraphviz,rsbml,rScudo,RTN,RTNduals,RTNsurvival,rTRM,rTRMui,rWikiPathways,SBGNview,SBMLR,ScISI,signet,sincell,SLGI,sparsenetgls,spatialHeatmap,SPIA,splineTimeR,spqn,SQUADD,ternarynet,ToPASeq,transcriptogramer,TreeAndLeaf,TRONCO,VennDetail", "id": "GraphAndNetwork" }, "children": [ ] }, { "data": "HiddenMarkovModel (13)", "attr": { "packageList": "AneuFinder,BUMHMM,chromstaR,DMCHMM,EBSeqHMM,frenchFISH,hummingbird,iCNV,infercnv,methimpute,nuCpos,STAN,TitanCNA", "id": "HiddenMarkovModel" }, "children": [ ] }, { "childnum": 0, "data": "MultidimensionalScaling", "children": [ ] }, { "data": "NeuralNetwork (2)", "attr": { "packageList": "COSNet,scAlign", "id": "NeuralNetwork" }, "children": [ ] }, { "data": "PatternLogic (4)", "attr": { "packageList": "GeneAccord,MouseFM,PathoStat,slinky", "id": "PatternLogic" }, "children": [ ] }, { "data": "PrincipalComponent (41)", "attr": { "packageList": "acde,AffiXcan,BatchQC,BiocSingular,ChromSCape,ClusterSignificance,COCOA,corral,DESeq2,DiscoRhythm,ENmix,esetVis,gcatest,GENESIS,Harman,lfa,made4,missRows,mogsa,MSstatsSampleSize,MultiBaC,OMICsPCA,padma,PathoStat,pathwayPCA,pcaExplorer,PCAtools,phantasus,phenopath,Pigengene,psichomics,ramwas,RiboProfiling,ropls,rqt,scPCA,scry,SNPRelate,STATegRa,tenXplore,TimeSeriesExperiment", "id": "PrincipalComponent" }, "children": [ ] }, { "data": "Regression (104)", "attr": { "packageList": "adaptest,AffiXcan,affylmGUI,AMARETTO,anota2seq,bacon,bambu,biobroom,BioMM,biotmle,BPRMeth,BUMHMM,calm,Cardinal,CeTF,CFAssay,chipenrich,CONFESS,consensus,CytoDx,dearseq,DESeq2,DMCFB,dmrseq,Doscheda,edge,edgeR,eisaR,ENmix,ExploreModelMatrix,fishpond,flowPloidy,fmrs,GAprediction,gCrisprTools,GEM,GENIE3,GenoGAM,GenomicOZone,genphen,gespeR,GIGSEA,glmGamPoi,glmSparseNet,GlobalAncova,globalSeq,GMRP,GNET2,gpls,graper,GRridge,gwasurvivr,hierinf,IgGeneUsage,IMAS,IVAS,kebabs,LEA,limma,limmaGUI,LinkHD,Melissa,metaCCA,metaseqR2,MethReg,methylGSA,methylSig,MetNet,mixOmics,NBSplice,netReg,NewWave,omicRexposome,OmicsLonDA,oppti,OPWeight,pathwayPCA,PathwaySplice,perturbatr,plrs,pmm,proDA,ResidualMatrix,RIVER,RNAdecay,rnaEditr,ropls,rqt,SAGx,scMAGeCK,sevenC,SIAMCAT,sparsenetgls,splineTimeR,SPONGE,SRGnet,switchde,timeOmics,topconfects,tradeSeq,trena,Trendy,variancePartition,weitrix", "id": "Regression" }, "children": [ ] }, { "data": "StructuralEquationModels (1)", "attr": { "packageList": "ASGSCA", "id": "StructuralEquationModels" }, "children": [ ] }, { "data": "SupportVectorMachine (11)", "attr": { "packageList": "cellity,EnMCB,genphen,kebabs,LedPred,procoil,rSWeeP,SC3,scmap,sigFeature,TNBC.CMS", "id": "SupportVectorMachine" }, "children": [ ] }, { "data": "Survival (29)", "attr": { "packageList": "CFAssay,ClassifyR,CoreGx,CrossICC,CytoDx,fmrs,GDCRNATools,geneClassifiers,glmSparseNet,GRridge,GSgalgoR,gwasurvivr,ivygapSE,maftools,messina,miRspongeR,MoonlightR,multiClust,OmicsLonDA,pathwayPCA,psichomics,RadioGx,rnaEditr,rqt,RTNsurvival,SCFA,simulatorZ,survtype,TCGAbiolinks", "id": "Survival" }, "children": [ ] }, { "data": "TimeCourse (57)", "attr": { "packageList": "acde,affylmGUI,AMARETTO,ASpli,CellNOptR,CellTrails,cellTree,CNORdt,CNORode,CoGAPS,CONFESS,ctsGE,cycle,dearseq,deltaGseg,DiscoRhythm,DMRcate,EBSeqHMM,edge,edgeR,EventPointer,flowTime,GOexpress,gprege,GRENITS,GRmetrics,ImpulseDE,ImpulseDE2,INSPEcT,limma,limmaGUI,LineagePulse,LiquidAssociation,maSigPro,metaseqR2,MethCP,Mfuzz,MOSim,MSstats,OmicsLonDA,plethy,rain,RmiR,RNAdecay,Rnits,RTCA,splineTimeR,TCseq,TDARACNE,tigre,timecourse,timeOmics,TimeSeriesExperiment,TimiRGeN,TMixClust,tradeSeq,Trendy", "id": "TimeCourse" }, "children": [ ] } ] }, { "data": "Technology (1251)", "attr": { "packageList": "ACME,amplican,CellaRepertorium,CoverageView,DMRScan,dupRadar,ELBOW,HiCBricks,iGC,LymphoSeq,MDTS,MetID,nondetects,openPrimeR,openPrimeRui,optimalFlow,pram,rSWeeP,scruff,sojourner,spkTools,TAPseq,wavClusteR", "id": "Technology" }, "children": [ { "childnum": 0, "data": "AnnotationHubSoftware", "children": [ ] }, { "data": "CRISPR (13)", "attr": { "packageList": "amplican,bcSeq,CRISPRseek,CrispRVariants,gCrisprTools,gemini,gscreend,GUIDEseq,MAGeCKFlute,mnem,multicrispr,scMAGeCK,TAPseq", "id": "CRISPR" }, "children": [ ] }, { "data": "ddPCR (2)", "attr": { "packageList": "ddPCRclust,twoddpcr", "id": "ddPCR" }, "children": [ ] }, { "childnum": 0, "data": "ExperimentHubSoftware", "children": [ ] }, { "data": "FlowCytometry (62)", "attr": { "packageList": "brainflowprobes,CATALYST,COMPASS,cydar,CytoDx,cytofast,cytolib,CytoML,CytoTree,DepecheR,diffcyt,distinct,flowAI,flowBeads,flowBin,flowCHIC,flowCL,flowClean,flowClust,flowCore,flowCut,flowCyBar,flowDensity,flowFit,flowFP,flowMap,flowMatch,flowMeans,flowMerge,flowPeaks,flowPloidy,flowPlots,FlowRepositoryR,FlowSOM,flowSpecs,flowSpy,flowStats,flowTime,flowTrans,flowType,flowUtils,flowViz,flowVS,flowWorkspace,GateFinder,ggcyto,immunoClust,infinityFlow,MACSQuantifyR,MetaCyto,MIMOSA,ncdfFlow,oneSENSE,openCyto,optimalFlow,PeacoQC,plotGrouper,RchyOptimyx,reconsi,SamSPECTRAL,scDataviz,Sconify", "id": "FlowCytometry" }, "children": [ ] }, { "data": "MassSpectrometry (103)", "attr": { "packageList": "adductomicsR,apComplex,artMS,Autotuner,BRAIN,CAMERA,Cardinal,CATALYST,cliqueMS,cosmiq,customProDB,DAPAR,DEP,DEqMS,DIAlignR,Doscheda,flagme,gaga,INDEED,IPO,isobar,IsoCorrectoR,IsoCorrectoRGUI,lipidr,LOBSTAHS,MAIT,marr,MassArray,MassSpecWavelet,Metab,metabCombiner,metabomxtr,metaMS,MetCirc,MetNet,MsCoreUtils,MSGFgui,MSGFplus,msImpute,msmsEDA,msmsTests,MSnbase,MSnID,MSPrep,msPurity,MSstats,MSstatsConvert,MSstatsPTM,MSstatsQC,MSstatsQCgui,MSstatsSampleSize,MSstatsTMT,MSstatsTMTPTM,mzID,mzR,ncGTW,peakPantheR,pepXMLTab,PGA,pgca,plgem,pmp,POMA,proBAMr,proBatch,PROcess,proDA,proFIA,pRoloc,Prostar,ProteoMM,ProtGenerics,qcmetrics,QFeatures,qPLEXanalyzer,Rdisop,Risa,RMassBank,rols,ropls,rpx,rTANDEM,sapFinder,scDataviz,scp,SDAMS,shinyTANDEM,SIMAT,SMAD,sparsenetgls,specL,Spectra,statTarget,SubCellBarCode,SWATH2stats,synapter,TargetSearch,tofsims,topdownr,TPP,wpm,xcms,yamss", "id": "MassSpectrometry" }, "children": [ { "data": "ImagingMassSpectrometry (2)", "attr": { "packageList": "Cardinal,tofsims", "id": "ImagingMassSpectrometry" }, "children": [ ] } ] }, { "data": "Microarray (435)", "attr": { "packageList": "a4,a4Base,a4Classif,a4Core,a4Preproc,a4Reporting,ABarray,acde,ACME,ADaCGH2,adaptest,adSplit,affxparser,affy,affycomp,AffyCompatible,affycoretools,AffyExpress,affyILM,affyio,affylmGUI,affyPara,affyPLM,affyQCReport,AffyRNADegradation,AGDEX,AgiMicroRna,AIMS,altcdfenvs,AMARETTO,AMOUNTAIN,annaffy,annmap,AnnotationDbi,annotationTools,anota,anota2seq,aroma.light,ArrayExpress,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,ARRmNormalization,attract,BAC,BatchQC,beadarray,BeadDataPackR,BgeeDB,BGmix,bgx,BHC,BicARE,bigmelon,biomvRCNS,BioNet,BioNetStat,biotmle,blima,BLMA,BrainStars,bridge,CAFE,calm,cancerclass,CausalR,ccmap,CCPROMISE,CellMapper,CellScore,cellTree,CeTF,CGHbase,CGHcall,cghMCR,CGHnormaliter,CGHregions,ChAMP,chopsticks,CINdex,clustifyr,cn.farms,CNTools,CNVRanger,codelink,coexnet,CoGAPS,cogena,coGPS,COHCAP,coMET,consensus,consensusOV,conumee,convert,Cormotif,CORREP,covEB,crlmm,CrossICC,crossmeta,ctc,cycle,daMA,dcGSA,DECIPHER,deco,DEGraph,DeMixT,DFP,diffcoexp,diffGeneAnalysis,discordant,DMRcate,DMRforPairs,DNAcopy,doppelgangR,DrugVsDisease,DTA,dualKS,dyebias,eegc,EGSEA,eisa,ELBOW,EMDomics,ENmix,EnrichmentBrowser,erccdashboard,ExiMiR,explorase,ExpressionView,fabia,factDesign,farms,fdrame,ffpe,flowVS,focalCall,frma,frmaTools,gage,gcrma,GCSscore,genArise,geneClassifiers,genefilter,GeneMeta,GeneNetworkBuilder,geneRecommender,GeneRegionScan,geNetClassifier,genoCN,genoset,GenRank,GEOquery,GEOsubmission,GLAD,Glimma,GlobalAncova,globaltest,GOexpress,GOFunction,goProfiles,goSTAG,GOstats,goTools,gpls,gprege,GSEABenchmarkeR,GSEAlm,GSRI,GSVA,Gviz,GWASTools,GWENA,Harman,Harshlight,HDTD,Heatplus,HELP,HEM,HMMcopy,HybridMTest,iBMQ,iCheck,iChip,iClusterPlus,IdeoViz,iGC,illuminaio,impute,interactiveDisplay,interactiveDisplayBase,InterMineR,IntramiRExploreR,inveRsion,IsoGeneGUI,ITALICS,iterativeBMA,iterativeBMAsurv,joda,KCsmart,KnowSeq,lapmix,les,limma,limmaGUI,lmdme,logitT,LPE,LPEadj,lumi,maanova,macat,maCorrPlot,made4,maigesPack,MANOR,mAPKL,maPredictDSC,marray,maSigPro,maskBAD,massiR,matchBox,MBCB,mBPCR,MCbiclust,mCSEA,mdp,mdqc,MEAL,MEAT,MEDIPS,MEDME,metaArray,metahdep,methyAnalysis,MethylAid,methylCC,Mfuzz,MGFM,MiChip,MIGSA,mimager,minet,minfi,MinimumDistance,MiPP,MiRaGE,mirIntegrator,miRNAtap,miRSM,miRspongeR,mixOmics,MmPalateMiRNA,MODA,motifStack,MotIV,Mulcom,multiscan,multtest,NanoStringQCPro,netbenchmark,netresponse,nnNorm,normalize450K,npGSEA,nucleR,OCplus,OGSA,oligo,OLIN,OLINgui,OrderedList,OutlierD,PAA,PADOG,pandaR,PathoStat,pathview,pcot2,PECA,pepStat,PGSEA,phantasus,phenoTest,piano,pickgene,Pigengene,plgem,PLPE,POST,prebs,PROMISE,puma,pvac,pvca,Pviz,pwrEWAS,qcmetrics,qpgraph,qsmooth,quantro,QUBIC,qusage,rain,rama,randRotation,RankProd,RBioinf,RBM,rbsurv,RDRToolbox,reb,recountmethylation,RefPlus,regsplice,REMP,ReportingTools,rGADEM,Ringo,RLMM,Rmagpie,RmiR,Rnits,ROntoTools,ROTS,RPA,RRHO,RTopper,runibic,SAGx,sampleClassifier,SBGNview,SCAN.UPC,scPCA,semisup,shinyMethyl,sigaR,sigFeature,siggenes,SIM,SimBindProfiles,simpleaffy,sizepower,SMAP,SNAGEE,snapCGH,snm,snpStats,spatialHeatmap,SpeCond,SPIA,spikeLI,spkTools,spotSegmentation,ssize,SSPA,STAN,Starr,stepNorm,STROMA4,sva,TDARACNE,TEQC,tigre,tilingArray,timecourse,timeOmics,TIN,TOAST,topGO,transcriptogramer,transite,tRanslatome,TransView,trigger,trio,tscR,tspair,TTMap,TurboNorm,twilight,variancePartition,vsn,wateRmelon,webbioc,XDE,xps,yaqcaffy", "id": "Microarray" }, "children": [ { "data": "ChipOnChip (8)", "attr": { "packageList": "ChIPanalyser,geneXtendeR,GenoGAM,profileplyr,puma,qsea,recoup,STAN", "id": "ChipOnChip" }, "children": [ ] }, { "data": "GenotypingArray (2)", "attr": { "packageList": "GDSArray,VariantExperiment", "id": "GenotypingArray" }, "children": [ ] }, { "data": "MethylationArray (33)", "attr": { "packageList": "AMARETTO,bacon,bigmelon,ChAMP,COCOA,coMET,compartmap,conumee,DMRcate,EnMCB,ENmix,EpiDISH,GEM,MBAmethyl,mCSEA,MEAT,MethReg,MethylAid,methylCC,MethylMix,methyvim,minfi,missMethyl,MoonlightR,normalize450K,recountmethylation,REMP,RnBeads,sesame,TCGAbiolinks,TCGAbiolinksGUI,TOAST,TurboNorm", "id": "MethylationArray" }, "children": [ ] }, { "data": "MicroRNAArray (4)", "attr": { "packageList": "AMARETTO,deco,limma,randRotation", "id": "MicroRNAArray" }, "children": [ ] }, { "data": "mRNAMicroarray (19)", "attr": { "packageList": "acde,affylmGUI,AMARETTO,CEMiTool,deco,discordant,erccdashboard,EventPointer,fcoex,goSTAG,GWENA,limma,limmaGUI,MetaVolcanoR,NanoStringQCPro,puma,sigFeature,topconfects,transite", "id": "mRNAMicroarray" }, "children": [ ] }, { "data": "MultiChannel (6)", "attr": { "packageList": "aroma.light,ELBOW,ENmix,minfi,REMP,snm", "id": "MultiChannel" }, "children": [ ] }, { "data": "OneChannel (75)", "attr": { "packageList": "ABarray,affxparser,affy,affycomp,AffyCompatible,affycoretools,AffyExpress,affyILM,affylmGUI,affyPLM,affyQCReport,AffyRNADegradation,AgiMicroRna,altcdfenvs,AMARETTO,annaffy,annmap,aroma.light,ArrayExpress,arrayQualityMetrics,ArrayTools,beadarray,BrainStars,bridge,CAFE,clippda,codelink,copa,CopyNumberPlots,crossmeta,cytomapper,diffcoexp,DMRcate,EGSEA,ELBOW,ENmix,ExiMiR,gaga,gage,gcrma,GCSscore,GeneRegionScan,GEOquery,GlobalAncova,globaltest,Harshlight,iCheck,iChip,karyoploteR,lapmix,limma,lmdme,lumi,makecdfenv,MSstatsTMTPTM,oligo,PAA,PADOG,PROMISE,puma,pvac,RefPlus,RLMM,SAGx,SCAN.UPC,simpleaffy,SNAGEE,snm,Starr,tilingArray,TurboNorm,vsn,webbioc,xps,yaqcaffy", "id": "OneChannel" }, "children": [ ] }, { "data": "ProprietaryPlatforms (8)", "attr": { "packageList": "affxparser,affylmGUI,altcdfenvs,AMARETTO,GCSscore,illuminaio,limma,metaseqR2", "id": "ProprietaryPlatforms" }, "children": [ ] }, { "childnum": 0, "data": "ReversePhaseProteinArray", "children": [ ] }, { "data": "TissueMicroarray (4)", "attr": { "packageList": "crossmeta,DeMixT,pwrEWAS,spatialHeatmap", "id": "TissueMicroarray" }, "children": [ ] }, { "data": "TwoChannel (63)", "attr": { "packageList": "AMARETTO,aroma.light,ArrayExpress,arrayQuality,arrayQualityMetrics,ARRmNormalization,beadarraySNP,bigmelon,bridge,ChAMP,convert,copa,cytomapper,daMA,diffcoexp,DMRcate,dyebias,EGSEA,ELBOW,ENmix,ExiMiR,gage,genArise,GEOquery,HELP,iCheck,limma,limmaGUI,lmdme,lumi,maigesPack,MANOR,marray,mCSEA,MethylAid,methylumi,minfi,MmPalateMiRNA,MSstatsTMTPTM,nnNorm,normalize450K,oligo,OLIN,OLINgui,PADOG,puma,rama,RegEnrich,REMP,Ringo,RnBeads,SCAN.UPC,shinyMethyl,skewr,SMAP,SNAGEE,snapCGH,snm,spotSegmentation,stepNorm,TurboNorm,vsn,wateRmelon", "id": "TwoChannel" }, "children": [ ] } ] }, { "data": "MicrotitrePlateAssay (14)", "attr": { "packageList": "bioassayR,ChemmineOB,ChemmineR,ddCt,eiR,fmcsR,HTqPCR,NormqPCR,ReadqPCR,sights,SLqPCR,splots,staRank,unifiedWMWqPCR", "id": "MicrotitrePlateAssay" }, "children": [ ] }, { "data": "qPCR (11)", "attr": { "packageList": "amplican,ddCt,DECIPHER,EasyqpcR,HTqPCR,miRcomp,nondetects,NormqPCR,ReadqPCR,SLqPCR,unifiedWMWqPCR", "id": "qPCR" }, "children": [ ] }, { "data": "SAGE (9)", "attr": { "packageList": "BADER,baySeq,DESeq,edgeR,GEOquery,MBttest,MiRaGE,rnaSeqMap,sagenhaft", "id": "SAGE" }, "children": [ ] }, { "data": "Sequencing (724)", "attr": { "packageList": "abseqR,ACE,adaptest,ADImpute,ALDEx2,AllelicImbalance,alpine,ALPS,AMARETTO,ANCOMBC,AneuFinder,AnnotationDbi,anota,anota2seq,APAlyzer,apeglm,appreci8R,ArrayExpressHTS,ASpediaFI,ASpli,ATACseqQC,BaalChIP,BADER,BadRegionFinder,bambu,bamsignals,BANDITS,basecallQC,BaseSpaceR,Basic4Cseq,BASiCS,batchelor,BatchQC,bayNorm,baySeq,BBCAnalyzer,bcSeq,BgeeDB,bigPint,biomvRCNS,BioNetStat,Biostrings,BioTIP,biotmle,BiSeq,BitSeq,blacksheepr,BPRMeth,BrainSABER,breakpointR,BRGenomics,BubbleTree,BUMHMM,CAGEfightR,CAGEr,calm,casper,celda,cellity,CellTrails,cellTree,CeTF,CexoR,cfDNAPro,Chicago,ChIPanalyser,ChIPComp,ChIPexoQual,ChIPQC,chipseq,ChIPSeqSpike,chromPlot,chromstaR,chromVAR,cicero,CINdex,cleanUpdTSeq,Clomial,clonotypeR,clstutils,clusterExperiment,clusterSeq,clustifyr,cn.mops,CNAnorm,CNVfilteR,CNVPanelizer,CNVrd2,COCOA,cogena,coMET,compEpiTools,ComplexHeatmap,consensusDE,consensusSeekeR,CopyNumberPlots,CorMut,corral,coseq,CountClust,CoverageView,csaw,CSSP,CSSQ,ctgGEM,ctsGE,customProDB,dada2,DaMiRseq,dasper,DBChIP,dcGSA,dearseq,debrowser,DECIPHER,deco,decompTumor2Sig,decontam,deepSNV,DEFormats,DegNorm,DeMixT,densvis,derfinder,derfinderHelper,derfinderPlot,DEScan2,DESeq,DESeq2,DEsingle,DEWSeq,DEXSeq,dexus,DiffBind,diffcoexp,diffHic,DirichletMultinomial,distinct,DMCFB,DMCHMM,DMRcaller,DMRcate,DMRScan,dmrseq,DNABarcodeCompatibility,DNABarcodes,doseR,dpeak,DRIMSeq,DropletUtils,DSS,dupRadar,EBSEA,EBSeq,EBSeqHMM,EDASeq,EDDA,edgeR,eegc,EGSEA,ELBOW,EnrichedHeatmap,ensembldb,epihet,esATAC,escape,EventPointer,exomeCopy,exomePeak2,FastqCleaner,fCCAC,FilterFFPE,fishpond,focalCall,FourCSeq,FRASER,gage,gcapc,GDSArray,GeneBreak,GeneMeta,GeneNetworkBuilder,geneRxCluster,genomation,GenomicAlignments,GenomicDataCommons,GenomicFeatures,GenomicFiles,GenomicOZone,GenomicRanges,GenomicScores,GenomicTuples,genotypeeval,genphen,GenRank,getDEE2,girafe,Glimma,globalSeq,gmoviz,GMRP,GOexpress,goseq,GOTHiC,GreyListChIP,groHMM,gtrellis,GUIDEseq,Guitar,Gviz,GWENA,hapFabia,HCABrowser,HCAExplorer,HDF5Array,HDTD,HelloRanges,HiCBricks,HiCcompare,hicrep,HilbertCurve,HiLDA,HIPPO,hiReadsProcessor,HiTC,HMMcopy,HTSFilter,hummingbird,icetea,ideal,iGC,IMAS,Imetagene,ImpulseDE2,InPAS,INSPEcT,InTAD,intansv,interactiveDisplay,interactiveDisplayBase,IntEREst,IONiseR,ISAnalytics,iSeq,ISoLDE,IVAS,ivygapSE,JunctionSeq,karyoploteR,KnowSeq,LedPred,lefser,levi,limma,LineagePulse,Linnorm,loci2path,LOLA,LowMACA,LymphoSeq,M3C,M3Drop,made4,MADSEQ,maftools,MBASED,mbkmeans,MBttest,mcaGUI,MDTS,MEB,MEDIPS,Melissa,metagene,metagene2,metagenomeFeatures,metagenomeSeq,metaSeq,metaseqR2,MethCP,methimpute,methInheritSim,methrix,MethTargetedNGS,methylCC,methylInheritance,methylKit,methylMnM,methylPipe,MethylSeekR,microbiome,microbiomeExplorer,MIRA,MiRaGE,miRNAtap,mixOmics,MLSeq,MMDiff2,Modstrings,monocle,mosaics,motifStack,mpra,MPRAnalyze,msa,multiHiCcompare,muscat,muscle,NADfinder,NarrowPeaks,NBAMSeq,netSmooth,NewWave,NOISeq,nucleoSim,nucleR,omicplotR,oncomix,ORFik,Organism.dplyr,Oscope,OTUbase,OUTRIDER,panelcn.mops,PathoStat,pathview,PathwaySplice,PCAN,peco,PERFect,periodicDNA,PGA,phemd,philr,phyloseq,PICS,PING,podkat,polyester,Polyfit,pram,prebs,preciseTAD,PrecisionTrialDrawer,primirTSS,profileplyr,PROPER,psichomics,PureCN,qckitfastq,QDNAseq,qrqc,qsea,qsmooth,QSutils,quantro,QuasR,r3Cseq,R453Plus1Toolbox,ramwas,randRotation,RareVariantVis,Rariant,Rbowtie,Rbowtie2,Rcade,recount,recount3,recoup,REDseq,regionReport,regsplice,REMP,RepViz,ReQON,restfulSE,Rfastp,rGADEM,rGREAT,Rhisat2,Rhtslib,RiboProfiling,riboSeqR,ribosomeProfilingQC,RJMCMCNucleosomes,RNAmodR,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,RNAprobR,rnaSeqMap,RNASeqR,RnaSeqSampleSize,RnBeads,roar,Rqc,rqt,rRDP,Rsamtools,Rsubread,RSVSim,rSWeeP,RTCGAToolbox,runibic,samExploreR,sangeranalyseR,sangerseqR,savR,SBGNview,Scale4C,scater,scCB2,scds,scGPS,schex,scHOT,scmap,scMerge,scone,SCOPE,scPCA,scPipe,scran,scRecover,scRepertoire,scruff,scry,scuttle,segmentSeq,selectKSigs,SeqArray,seqbias,seqCAT,seqCNA,SeqGate,SeqGSEA,seqplots,seqsetvis,seqTools,SeqVarTools,ShortRead,SIAMCAT,SICtools,signatureSearch,SimFFPE,SIMLR,sincell,slalom,slingshot,SMITE,snapcount,snifter,soGGi,SomaticSignatures,Spaniel,spatialHeatmap,SpectralTAD,splatter,SplicingGraphs,splots,SPsimSeq,SRAdb,ssviz,STAN,Structstrings,StructuralVariantAnnotation,subSeq,SummarizedExperiment,survtype,Sushi,sva,systemPipeR,systemPipeShiny,TADCompare,TAPseq,TarSeqQC,TCC,TCGAbiolinks,TCGAbiolinksGUI,TCseq,TEQC,TFEA.ChIP,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,timeOmics,TimeSeriesExperiment,TissueEnrich,TitanCNA,tomoda,tracktables,tradeSeq,transcriptR,TransView,traseR,TSRchitect,TVTB,tweeDEseq,Ularcirc,UMI4Cats,VariantAnnotation,VariantExperiment,VariantFiltering,VariantTools,VCFArray,velociraptor,VERSO,VplotR,wavClusteR,wiggleplotr,Wrench,XBSeq,XCIR,YAPSA,yarn,zinbwave", "id": "Sequencing" }, "children": [ { "data": "ATACSeq (19)", "attr": { "packageList": "ALPS,ATACseqQC,bcSeq,BiFET,BRGenomics,ChromSCape,chromstaR,cicero,COCOA,compartmap,DiffBind,esATAC,metaseqR2,mnem,recoup,RepViz,scBFA,spatialHeatmap,VplotR", "id": "ATACSeq" }, "children": [ ] }, { "data": "ChIPSeq (89)", "attr": { "packageList": "ALDEx2,ALPS,atSNP,BaalChIP,BRGenomics,CeTF,ChIC,ChIPanalyser,ChIPComp,chipenrich,ChIPexoQual,ChIPpeakAnno,ChIPQC,ChIPseeker,chipseq,ChIPseqR,ChIPSeqSpike,ChIPsim,ChIPXpress,ChromSCape,chromstaR,COCOA,coMET,consensusSeekeR,CoverageView,CSAR,csaw,CSSP,CSSQ,DBChIP,debrowser,derfinder,DESeq,DESeq2,DiffBind,dpeak,EDDA,edgeR,epigenomix,FunChIP,gcapc,geneXtendeR,GenoGAM,GreyListChIP,iASeq,Imetagene,InTAD,iSeq,karyoploteR,LedPred,Linnorm,LOLA,marr,MEDIPS,metagene,metagene2,metaseqR2,MIRA,MMDiff2,motifbreakR,motifStack,MotIV,NarrowPeaks,normr,nucleR,profileplyr,qsea,QuasR,Rcade,recoup,regioneR,RepViz,rGADEM,RJMCMCNucleosomes,Rsubread,samExploreR,seqplots,seqsetvis,sevenC,similaRpeak,soGGi,STAN,systemPipeR,TCseq,TFEA.ChIP,TFHAZ,TransView,vulcan,wiggleplotr", "id": "ChIPSeq" }, "children": [ ] }, { "childnum": 0, "data": "DenovoGenome", "children": [ ] }, { "childnum": 0, "data": "DenovoTranscriptome", "children": [ ] }, { "data": "DNASeq (36)", "attr": { "packageList": "ACE,ALDEx2,ATACseqQC,breakpointR,Clomial,CNAnorm,CNVfilteR,coMET,CopyNumberPlots,dearseq,DEComplexDisease,decompTumor2Sig,esATAC,GeneBreak,GenVisR,karyoploteR,maftools,MMAPPR2,mnem,NADfinder,omicplotR,QDNAseq,QSutils,RcwlPipelines,regioneR,samExploreR,SCOPE,semisup,SigsPack,spatialHeatmap,SPsimSeq,TCGAbiolinksGUI,TitanCNA,TVTB,uSORT,YAPSA", "id": "DNASeq" }, "children": [ ] }, { "data": "DNaseSeq (3)", "attr": { "packageList": "BiFET,COCOA,esATAC", "id": "DNaseSeq" }, "children": [ ] }, { "data": "ExomeSeq (10)", "attr": { "packageList": "Clomial,CODEX,coMET,CopywriteR,exomePeak2,globalSeq,iCNV,RVS,TitanCNA,Uniquorn", "id": "ExomeSeq" }, "children": [ ] }, { "data": "HiC (21)", "attr": { "packageList": "bnbc,Chicago,diffHic,GenomicInteractions,GOTHiC,HiCBricks,HiCcompare,hicrep,HiTC,idr2d,InTAD,InteractionSet,MACPET,multiHiCcompare,Pi,preciseTAD,R3CPET,sevenC,SpectralTAD,Sushi,TADCompare", "id": "HiC" }, "children": [ ] }, { "data": "MethylSeq (32)", "attr": { "packageList": "BEAT,biscuiteer,BiSeq,ChromSCape,COCOA,COHCAP,coMET,compartmap,epihet,exomePeak2,GEM,Guitar,karyoploteR,LOLA,methInheritSim,methylCC,methylInheritance,methylKit,methylPipe,MethylSeekR,methylSig,methyvim,MIRA,MPFE,msgbsR,padma,QuasR,regioneR,Repitools,RnBeads,systemPipeR,TransView", "id": "MethylSeq" }, "children": [ ] }, { "childnum": 0, "data": "MicrobialStrain", "children": [ ] }, { "data": "Microbiome (33)", "attr": { "packageList": "ALDEx2,ANCOMBC,animalcules,BDMMAcorrect,biomformat,combi,countsimQC,dada2,DECIPHER,decontam,DirichletMultinomial,gramm4R,lefser,Maaslin2,metagenomeFeatures,metagenomeSeq,microbiome,microbiomeDASim,microbiomeExplorer,MicrobiotaProcess,MMUPHin,omicplotR,OmicsLonDA,PathoStat,PERFect,philr,phyloseq,RCM,reconsi,rRDP,SIAMCAT,sparseDOSSA,TimeSeriesExperiment", "id": "Microbiome" }, "children": [ ] }, { "data": "miRNA (12)", "attr": { "packageList": "globalSeq,isomiRs,miRBaseConverter,miRLAB,miRNAmeConverter,miRNApath,miRNAtap,rcellminer,Roleswitch,SpidermiR,TargetScore,TimiRGeN", "id": "miRNA" }, "children": [ ] }, { "childnum": 0, "data": "MNaseSeq", "children": [ ] }, { "data": "PooledScreens (8)", "attr": { "packageList": "gCrisprTools,gscreend,MAGeCKFlute,MMAPPR2,mnem,pogos,scMAGeCK,TAPseq", "id": "PooledScreens" }, "children": [ ] }, { "data": "RiboSeq (6)", "attr": { "packageList": "coMET,ORFik,RiboProfiling,riboSeqR,ribosomeProfilingQC,systemPipeR", "id": "RiboSeq" }, "children": [ ] }, { "data": "RIPSeq (3)", "attr": { "packageList": "BiFET,normr,wavClusteR", "id": "RIPSeq" }, "children": [ ] }, { "data": "RNASeq (314)", "attr": { "packageList": "aggregateBioVar,AIMS,ALDEx2,alpine,AMARETTO,Anaquin,anota2seq,APAlyzer,apeglm,ArrayExpressHTS,ASpli,attract,bacon,BADER,ballgown,bambu,BANDITS,Basic4Cseq,BASiCS,batchelor,BatchQC,bayNorm,BgeeCall,bigPint,BioNetStat,BioTIP,biotmle,BitSeq,blacksheepr,BPRMeth,BRGenomics,BUMHMM,BUSpaRse,calm,CancerInSilico,caOmicsV,casper,CausalR,CellaRepertorium,cellity,cellTree,CEMiTool,CeTF,CHETAH,clusterExperiment,CNVRanger,CoGAPS,coMET,compcodeR,CONFESS,consensus,coseq,CountClust,countsimQC,covEB,CoverageView,cqn,CrossICC,ctgGEM,cTRAP,ctsGE,customProDB,DaMiRseq,dasper,dcGSA,dearseq,debrowser,deco,DEFormats,DegNorm,DEGreport,DEGseq,DepecheR,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEsingle,DEsubs,DEXSeq,dexus,diffcoexp,discordant,distinct,dittoSeq,doppelgangR,DRIMSeq,DropletUtils,DSS,Dune,dupRadar,easyRNASeq,EBSeq,EBSeqHMM,EDASeq,EDDA,edgeR,eegc,EGSEA,eisaR,ELBOW,EnhancedVolcano,EnrichmentBrowser,erccdashboard,ERSSA,EventPointer,ExCluster,exomePeak2,fcoex,fishpond,FRASER,gage,gCrisprTools,GDCRNATools,GeneStructureTools,GenomicAlignments,GenomicOZone,Glimma,glmGamPoi,globalSeq,GOexpress,goseq,goSTAG,GRridge,GSEABenchmarkeR,Guitar,GWENA,HDF5Array,HTSFilter,iASeq,iasva,icetea,ideal,IHW,ILoReg,IMAS,InPAS,INSPEcT,InTAD,IntEREst,IsoformSwitchAnalyzeR,ISoLDE,isomiRs,IVAS,JunctionSeq,kissDE,KnowSeq,limma,Linnorm,M3C,M3Drop,marr,MAST,mbkmeans,MCbiclust,megadepth,Melissa,metaSeq,metaseqR,metaseqR2,MetaVolcanoR,mfa,MGFR,MIGSA,MiRaGE,MLSeq,MMAPPR2,mnem,monocle,MOSim,NBAMSeq,NBSplice,netSmooth,NOISeq,omicplotR,OPWeight,ORFik,Oscope,OUTRIDER,padma,PAIRADISE,PathoStat,pathview,PathwaySplice,pcaExplorer,PCAtools,peco,PGA,phantasus,phenopath,Pigengene,Polyfit,pram,prebs,primirTSS,Prize,proActiv,PROPER,psichomics,qsmooth,QuasR,qusage,randRotation,RcwlPipelines,recount,recount3,recoup,RegEnrich,regionReport,regsplice,ReportingTools,rgsepd,RNAAgeCalc,RNAdecay,rnaEditr,RNAsense,rnaseqcomp,rnaSeqMap,RNASeqPower,RNASeqR,RnaSeqSampleSize,ROTS,Rsubread,RTCGA,RUVSeq,samExploreR,sampleClassifier,sapFinder,sarks,SBGNview,SC3,SCAN.UPC,scater,scCB2,scDataviz,scDblFinder,scDD,scde,scds,scFeatureFilter,scHOT,scMAGeCK,scmap,scMerge,SCnorm,scone,scPCA,scPipe,scran,scRecover,scruff,scry,scuttle,SeqGate,SeqGSEA,seqplots,SGSeq,SigFuge,sincell,SingleCellSignalR,slalom,slingshot,SMITE,snapcount,Spaniel,SpatialCPie,splatter,SplicingGraphs,SPLINTER,SPsimSeq,sSeq,SSPA,ssPATHS,ssviz,STAN,strandCheckR,STROMA4,subSeq,sva,SVAPLSseq,switchde,systemPipeR,TCC,TCseq,TFEA.ChIP,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,TimeSeriesExperiment,tomoda,ToPASeq,topconfects,tradeSeq,transcriptogramer,transcriptR,TransView,Trendy,tweeDEseq,tximeta,tximport,uSORT,variancePartition,vasp,VaSP,vidger,wavClusteR,weitrix,wiggleplotr,XBSeq,XCIR,XINA,zFPKM,zinbwave", "id": "RNASeq" }, "children": [ ] }, { "data": "SangerSeq (2)", "attr": { "packageList": "FastqCleaner,sangeranalyseR", "id": "SangerSeq" }, "children": [ ] }, { "data": "SmallRNA (1)", "attr": { "packageList": "srnadiff", "id": "SmallRNA" }, "children": [ ] }, { "data": "TargetedResequencing (6)", "attr": { "packageList": "CellaRepertorium,Clomial,CopywriteR,LymphoSeq,MDTS,TarSeqQC", "id": "TargetedResequencing" }, "children": [ ] }, { "data": "WholeGenome (32)", "attr": { "packageList": "ACE,AneuFinder,BadRegionFinder,cfDNAPro,CNAnorm,contiBAIT,DECIPHER,DEComplexDisease,DMRcate,DMRScan,dmrseq,GeneBreak,GenoGAM,globalSeq,iCNV,LowMACA,MEAL,MethCP,methInheritSim,methylCC,methylInheritance,podkat,PrecisionTrialDrawer,RareVariantVis,rGREAT,RVS,samExploreR,SCOPE,sscu,TitanCNA,TVTB,Uniquorn", "id": "WholeGenome" }, "children": [ ] } ] }, { "data": "SingleCell (144)", "attr": { "packageList": "ADImpute,aggregateBioVar,alevinQC,AneuFinder,AUCell,BASiCS,batchelor,BayesSpace,bayNorm,BEARscc,bluster,BPRMeth,breakpointR,BUSpaRse,CancerInSilico,CATALYST,ccfindR,celaref,celda,CellaRepertorium,CellMixS,CellTrails,CeTF,CHETAH,ChromSCape,chromVAR,cicero,CiteFuse,clusterExperiment,clustifyr,corral,countsimQC,ctgGEM,cydar,cytomapper,densvis,DepecheR,DEsingle,diffcyt,distinct,dittoSeq,DropletUtils,Dune,escape,FCBF,fcoex,fishpond,flowSpecs,glmGamPoi,HCABrowser,HDF5Array,HIPPO,ILoReg,immunoClust,infercnv,infinityFlow,ISAnalytics,iSEE,iSEEu,LACE,LineagePulse,Linnorm,LoomExperiment,MAST,mbkmeans,Melissa,MetaNeighbor,mfa,mitch,mnem,muscat,Nebulosa,netSmooth,NewWave,OMICsPCA,PCAtools,peco,phemd,phenopath,PubScore,restfulSE,RGMQL,ROSeq,Rsubread,SC3,scAlign,scater,scBFA,scCB2,scClassify,scDataviz,scDblFinder,scDD,scds,scFeatureFilter,scGPS,schex,scHOT,scMAGeCK,scmap,scMerge,scmeth,SCnorm,scone,Sconify,SCOPE,scp,scPipe,scran,scRecover,scRepertoire,scruff,scry,scTensor,scTGIF,scTHI,scuttle,SDAMS,SIMD,SIMLR,SingleCellExperiment,SingleCellSignalR,singleCellTK,SingleR,slalom,slingshot,snifter,Spaniel,SpatialExperiment,spatialHeatmap,spicyR,splatter,SPsimSeq,switchde,TAPseq,tenXplore,tradeSeq,TRONCO,tximeta,velociraptor,waddR,weitrix,zellkonverter,zinbwave", "id": "SingleCell" }, "children": [ ] } ] }, { "data": "WorkflowStep (1081)", "attr": { "packageList": "AUCell,BUSpaRse,ChIPanalyser,DRIMSeq,GladiaTOX,GUIDEseq,iGC,metaseqR,metaseqR2,MetID,nanotatoR,nondetects,omicRexposome,pgca,phosphonormalizer,pipeFrame,plyranges,Rcwl,RcwlPipelines,rDGIdb,RepViz,RNAdecay,RNAmodR,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,SCANVIS,scruff,sojourner,struct,structToolbox,TCGAutils,tRNAscanImport", "id": "WorkflowStep" }, "children": [ { "data": "Alignment (80)", "attr": { "packageList": "amplican,ASpli,BadRegionFinder,bambu,bamsignals,Basic4Cseq,BBCAnalyzer,bcSeq,Biostrings,chimeraviz,ChIPanalyser,ChIPexoQual,DECIPHER,DegNorm,DIAlignR,diffHic,DiffLogo,DominoEffect,esATAC,FilterFFPE,FScanR,GenomicAlignments,ggtree,gmapR,GreyListChIP,Guitar,Imetagene,IMMAN,IntEREst,KnowSeq,Logolas,LowMACA,LymphoSeq,metagene,metagene2,MethTargetedNGS,motifStack,msa,muscle,ncGTW,normr,nucleoSim,odseq,ORFik,OUTRIDER,periodicDNA,QSutils,QuasR,R4RNA,Rbowtie,Rbowtie2,RcwlPipelines,recoup,Rhisat2,RiboProfiling,RNASeqR,Rsamtools,Rsubread,rSWeeP,samExploreR,sangeranalyseR,SCOPE,scruff,segmentSeq,seqcombo,SICtools,SimFFPE,singleCellTK,sitePath,strandCheckR,Structstrings,systemPipeR,TarSeqQC,TFBSTools,traseR,treeio,TVTB,UMI4Cats,VplotR", "id": "Alignment" }, "children": [ { "data": "MultipleSequenceAlignment (12)", "attr": { "packageList": "bcSeq,ggtree,LowMACA,LymphoSeq,msa,muscle,odseq,R4RNA,rfaRm,Rsubread,sitePath,treeio", "id": "MultipleSequenceAlignment" }, "children": [ ] } ] }, { "data": "Annotation (124)", "attr": { "packageList": "AffyExpress,altcdfenvs,annaffy,annmap,annotate,AnnotationDbi,AnnotationFilter,AnnotationForge,annotationTools,annotatr,APAlyzer,ArrayTools,artMS,ASpediaFI,biobtreeR,BiocIO,biomaRt,brendaDb,BridgeDbR,BSgenome,CAGEfightR,Category,categoryCompare,cellbaseR,ChIPpeakAnno,ChIPseeker,chromPlot,ChromSCape,circRNAprofiler,clusterProfiler,clustifyr,crossmeta,csaw,DeepBlueR,DelayedArray,DMRforPairs,DOSE,ecolitk,enrichplot,ensemblVEP,ENVISIONQuery,escape,FGNet,FScanR,FunciSNP,gaggle,garfield,GeneTonic,geneXtendeR,genomation,GenomeInfoDb,genomes,GenomicFeatures,GenomicOZone,GenomicRanges,GenomicScores,ggtree,ggtreeExtra,GOexpress,GOpro,goProfiles,GOSemSim,GOstats,HDF5Array,HelloRanges,hiAnnotator,hypeR,iBBiG,intansv,IsoformSwitchAnalyzeR,KEGGREST,matchBox,mdgsa,MeSHDbi,meshes,meshr,metagenomeFeatures,miRNApath,mygene,myvariant,occugene,OmaDB,OmicCircos,Onassis,Organism.dplyr,OrganismDbi,packFinder,PCAN,pdInfoBuilder,PloGO2,podkat,RBioinf,rDGIdb,ReactomePA,rfPred,RIPAT,Risa,RNAither,rnaSeqMap,rols,rrvgo,rsemmed,rtracklayer,SCANVIS,scRepertoire,SemDist,sevenC,simpleaffy,SingleR,SplicingGraphs,StructuralVariantAnnotation,SummarizedExperiment,SWATH2stats,treeio,tximeta,Ularcirc,uncoverappLib,UniProt.ws,VariantAnnotation,VariantExperiment,VariantFiltering,ViSEAGO,xmapbridge,yarn", "id": "Annotation" }, "children": [ ] }, { "data": "BatchEffect (52)", "attr": { "packageList": "affylmGUI,alpine,AMARETTO,anota2seq,bacon,batchelor,BatchQC,BDMMAcorrect,BEclear,BUScorrect,CellMixS,ChromSCape,corral,CrossICC,crossmeta,DegNorm,edgeR,ENmix,erccdashboard,fishpond,gcapc,genotypeeval,Harman,iasva,IsoformSwitchAnalyzeR,KnowSeq,limma,limmaGUI,Linnorm,metaseqR2,MethylAid,MMUPHin,MultiBaC,NewWave,OpenStats,pmp,proBatch,pvca,qsmooth,ramwas,randRotation,ResidualMatrix,RnBeads,scBFA,scMerge,scran,sights,statTarget,sva,SVAPLSseq,variancePartition,wpm", "id": "BatchEffect" }, "children": [ ] }, { "data": "ExperimentalDesign (22)", "attr": { "packageList": "ASAFE,brainflowprobes,CATALYST,countsimQC,EDDA,ExploreModelMatrix,gCrisprTools,kissDE,MOSim,MSstatsSampleSize,Omixer,OSAT,regsplice,ResidualMatrix,rexposome,RNASeqR,RnaSeqSampleSize,SWATH2stats,SynMut,systemPipeShiny,wpm,XBSeq", "id": "ExperimentalDesign" }, "children": [ ] }, { "data": "GenomeBrowsers (2)", "attr": { "packageList": "CAGEfightR,igvR", "id": "GenomeBrowsers" }, "children": [ ] }, { "data": "MultipleComparison (163)", "attr": { "packageList": "abseqR,adaptest,affylmGUI,AMARETTO,artMS,bacon,bambu,BANDITS,baySeq,BGmix,bigPint,biobroom,bioCancer,bumphunter,calm,categoryCompare,CellScore,ChIPComp,ChIPseeker,ChromSCape,chromstaR,chromswitch,clippda,Clomial,clusterProfiler,clusterSeq,cnvGSA,CoGAPS,CompGO,consensusDE,consensusSeekeR,csaw,ctgGEM,cydar,cytomapper,deco,DEqMS,diffHic,DiffLogo,distinct,dks,DMRcate,dmrseq,DOSE,DRIMSeq,EBSeq,EBSeqHMM,edge,edgeR,EGSEA,erccdashboard,ERSSA,fabia,fdrame,fishpond,flowMap,gaga,gage,gCrisprTools,GeneOverlap,GEWIST,GGPA,globalSeq,GOexpress,GOpro,goProfiles,GOstats,GPA,Harman,HTqPCR,iGC,IHW,Imetagene,InterMineR,IsoformSwitchAnalyzeR,ISoLDE,IWTomics,LBE,limma,limmaGUI,LinkHD,made4,matchBox,MBttest,mCSEA,meshes,metagene,metagene2,metagenomeSeq,MetaNeighbor,metaseqR2,microbiomeExplorer,MicrobiotaProcess,MineICA,mixOmics,MmPalateMiRNA,monocle,MouseFM,msa,Mulcom,MultiMed,multtest,nearBynding,NormalyzerDE,normr,OCplus,omicade4,omicRexposome,OMICsPCA,onlineFDR,openPrimeR,OPWeight,OrderedList,OVESEG,parody,PathNet,pathwayPCA,phemd,phenoTest,PhyloProfile,phyloseq,PloGO2,plotGrouper,Prize,PROMISE,psichomics,qsmooth,quantro,QUBIC,R4RNA,rain,RBioinf,ReactomePA,reconsi,rexposome,SAGx,scDD,Sconify,segmentSeq,semisup,seqsetvis,SIAMCAT,siggenes,sights,sigPathway,SimFFPE,similaRpeak,snm,SpeCond,ssviz,staRank,statTarget,sva,swfdr,timeOmics,topconfects,tradeSeq,TransView,TTMap,TVTB,twilight,unifiedWMWqPCR,ViSEAGO", "id": "MultipleComparison" }, "children": [ ] }, { "data": "Normalization (129)", "attr": { "packageList": "ACME,affylmGUI,alpine,AMARETTO,ANCOMBC,anota2seq,artMS,AUCell,bambu,BASiCS,batchelor,bayNorm,bigPint,blima,bnbc,BRGenomics,CAGEfightR,CAGEr,Cardinal,CATALYST,cellity,CeTF,ChAMP,ChIPSeqSpike,ChromSCape,CNAnorm,CNVPanelizer,CODEX,coexnet,conumee,CrossICC,csaw,CSSQ,cytomapper,DAPAR,DegNorm,DEqMS,DESeq2,DEsubs,diffHic,diffuStats,Doscheda,EDDA,edgeR,EnMCB,ENmix,exomePeak2,fishpond,flowSpecs,funtooNorm,gCrisprTools,GladiaTOX,Harman,HiCcompare,HTSFilter,IntEREst,KnowSeq,limma,limmaGUI,Linnorm,lipidr,Maaslin2,MACSQuantifyR,MAGeCKFlute,MANOR,MBQN,MEAT,MEB,metagenomeSeq,metaseqR,metaseqR2,microbiomeExplorer,minfi,missMethyl,MSstats,MSstatsTMTPTM,multiHiCcompare,NanoStringDiff,NanoStringQCPro,netSmooth,normalize450K,NormalyzerDE,normr,phantasus,phosphonormalizer,Pigengene,POMA,proBatch,proDA,Prostar,ProteoMM,qPLEXanalyzer,qsea,qsmooth,quantro,ramwas,randRotation,RNAdecay,RNAprobR,RNASeqR,Rnits,RUVcorr,RUVnormalize,scater,SCBN,scMerge,SCnorm,scone,SCOPE,scran,scry,scuttle,sigFeature,sights,slalom,Spaniel,spqn,statTarget,sva,SVAPLSseq,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,TimeSeriesExperiment,TurboNorm,UMI4Cats,variancePartition,Wrench,yarn", "id": "Normalization" }, "children": [ ] }, { "data": "Pathways (180)", "attr": { "packageList": "ADAM,ADAMgui,annaffy,annotate,ASpediaFI,ASSIGN,attract,bioCancer,BioCor,BioMM,BioNetStat,BLMA,Category,categoryCompare,CellNOptR,CEMiTool,ChromSCape,CHRONOS,clusterProfiler,cogena,coRdon,cpvSNP,cTRAP,DART,DEsubs,DOSE,edgeR,EGSEA,EmpiricalBrownsMethod,EnrichmentBrowser,enrichplot,epiNEM,escape,esetVis,famat,fastLiquidAssociation,fcoex,FELLA,FGNet,fgsea,gage,GeneAccord,GeneTonic,gep2pep,GlobalAncova,globaltest,GOexpress,GOFunction,goProfiles,GOSemSim,GOSim,GOstats,graphite,GRridge,GSEABenchmarkeR,gsean,GSReg,GSVA,GWENA,hipathia,hypeR,InterMineR,joda,KEGGgraph,KEGGlincs,keggorthology,KEGGprofile,KEGGREST,KnowSeq,LiquidAssociation,MAGeCKFlute,mdgsa,MetaboSignal,methylGSA,MethylMix,mgsa,mirIntegrator,miRNApath,MmPalateMiRNA,mnem,MoonlightR,multiGSEA,NCIgraph,ndexr,netboxr,NetPathMiner,npGSEA,occugene,OmnipathR,oppar,padma,PAST,Path2PPI,PathNet,pathRender,pathVar,pathview,pathwayPCA,PathwaySplice,paxtoolsr,PCAN,Pi,piano,PloGO2,PoTRA,PPInfer,qpgraph,RandomWalkRestartMH,ReactomePA,rGREAT,RNASeqR,rrvgo,rsbml,rsemmed,safe,SAGx,SBGNview,SBMLR,sigaR,signet,ssPATHS,StarBioTrek,TCGAbiolinks,TCGAbiolinksGUI,TimeSeriesExperiment,TimiRGeN,ToPASeq,transomics2cytoscape", "id": "Pathways" }, "children": [ { "data": "BioCarta (7)", "attr": { "packageList": "graphite,loci2path,multiGSEA,padma,PoTRA,RandomWalkRestartMH,UniProt.ws", "id": "BioCarta" }, "children": [ ] }, { "data": "GO (72)", "attr": { "packageList": "annaffy,annotate,BgeeDB,BiocSet,BioMM,Category,categoryCompare,cellTree,ClusterJudge,clusterProfiler,cogena,CompGO,DAPAR,diffloop,EGSEA,enrichplot,ExpressionView,famat,FELLA,FGNet,FoldGO,gage,GAPGOM,GDCRNATools,GeneTonic,geneXtendeR,gep2pep,globaltest,GOexpress,GOfuncR,GOFunction,GOpro,goProfiles,GOSemSim,goseq,GOSim,goSTAG,GOstats,GOsummaries,goTools,GRridge,GSEABase,GWENA,hipathia,interactiveDisplay,interactiveDisplayBase,InterMineR,KnowSeq,mdgsa,MetaNeighbor,mgsa,MmPalateMiRNA,NoRCE,OmaDB,ontoProc,PathwaySplice,PloGO2,Prostar,RCAS,Rcpi,ReportingTools,rGREAT,RNAither,RNASeqR,rols,rrvgo,SemDist,signatureSearch,simplifyEnrichment,tRanslatome,UniProt.ws,ViSEAGO", "id": "GO" }, "children": [ ] }, { "data": "KEGG (52)", "attr": { "packageList": "ADAM,ADAMgui,ASpediaFI,attract,BiocSet,BPRMeth,CHRONOS,clusterProfiler,cogena,coRdon,dearseq,DEsubs,EGSEA,enrichplot,ExpressionView,famat,FELLA,GDCRNATools,graphite,GRridge,GSEABase,InterMineR,KEGGgraph,KEGGlincs,keggorthology,KEGGprofile,KEGGREST,MAGeCKFlute,Melissa,MetaboSignal,MetID,MIGSA,mirIntegrator,MLP,netboxr,PathNet,pathprint,paxtoolsr,pcot2,PloGO2,PoTRA,RandomWalkRestartMH,RNASeqR,SAGx,scBFA,signatureSearch,signet,StarBioTrek,transomics2cytoscape,UniProt.ws,vasp,VaSP", "id": "KEGG" }, "children": [ ] }, { "childnum": 0, "data": "NCINatureCurated", "children": [ ] }, { "data": "Reactome (19)", "attr": { "packageList": "ASpediaFI,attract,bioCancer,clusterProfiler,famat,graphite,InterMineR,MetaboSignal,mitch,MLP,multiGSEA,netboxr,pathprint,paxtoolsr,PoTRA,RandomWalkRestartMH,ReactomeGSA,ReactomePA,slalom", "id": "Reactome" }, "children": [ ] } ] }, { "data": "Preprocessing (234)", "attr": { "packageList": "a4Preproc,ABarray,ADImpute,affy,affycomp,AffyExpress,affyILM,affylmGUI,affyPara,affyPLM,AffyRNADegradation,AgiMicroRna,AlpsNMR,altcdfenvs,AMARETTO,Anaquin,aroma.light,ArrayTools,ARRmNormalization,ballgown,BatchQC,beadarray,beadarraySNP,BEclear,bigmelon,bigPint,biovizBase,blima,bnbc,BUS,CAGEfightR,CAGEr,CATALYST,cellHTS2,cellity,CGHcall,CGHnormaliter,ChromSCape,clippda,CluMSID,codelink,conumee,CopywriteR,corral,covEB,cqn,crlmm,CrossICC,crossmeta,cytolib,DAPAR,DeepBlueR,DEGseq,DEqMS,DEsingle,diffHic,diffloop,DMRcate,DNABarcodeCompatibility,DNABarcodes,Doscheda,dyebias,easyRNASeq,EDASeq,ENmix,esATAC,ExiMiR,exomePeak2,farms,FilterFFPE,flowCut,flowWorkspace,focalCall,FourCSeq,frenchFISH,frma,frmaTools,funtooNorm,gCrisprTools,gcrma,genArise,gespeR,GGPA,GladiaTOX,GOTHiC,GPA,gprege,GreyListChIP,Harman,Harshlight,HELP,hiReadsProcessor,HMMcopy,HTqPCR,HTSFilter,iasva,iBMQ,iCheck,imageHTS,IsoCorrectoR,IsoCorrectoRGUI,KnowSeq,limma,limmaGUI,lumi,maCorrPlot,MACSQuantifyR,maigesPack,makecdfenv,MANOR,marray,MBCB,MBQN,MEAT,MEDIPS,megadepth,MetaCyto,metaseqR,metaseqR2,methylumi,Mfuzz,MiChip,minfi,miRcomp,miRNAmeConverter,MmPalateMiRNA,MSPrep,multiscan,NanoStringQCPro,netprioR,netSmooth,nnNorm,nondetects,normalize450K,normr,NTW,oligo,OLIN,OLINgui,openCyto,PeacoQC,PepsNMR,pepStat,piano,POMA,prebs,primirTSS,proActiv,proBatch,proFIA,Prostar,puma,QDNAseq,qpcrNorm,qPLEXanalyzer,qrqc,qsea,qsmooth,quantro,QuasR,r3Cseq,R4RNA,rama,ramwas,randRotation,RBioinf,Rbowtie2,rCGH,RcwlPipelines,recoup,REDseq,RefPlus,REMP,ReQON,Rfastp,Ringo,RNAinteract,RNAither,RnBeads,RPA,Rsubread,RTCGA,RUVSeq,SAGx,samExploreR,sangeranalyseR,SCAN.UPC,scater,scCB2,scDblFinder,scds,scFeatureFilter,scmap,scmeth,scone,scp,scPipe,scRecover,scruff,scsR,scuttle,sesame,shinyMethyl,SIAMCAT,sights,simpleaffy,skewr,snapCGH,snm,Spaniel,spotSegmentation,srnadiff,Starr,statTarget,stepNorm,sva,SWATH2stats,synlet,SynMut,TargetSearch,TCGAutils,tilingArray,tRNAscanImport,TurboNorm,tximeta,tximport,UMI4Cats,variancePartition,vasp,VaSP,vsn,wateRmelon,xps,yarn", "id": "Preprocessing" }, "children": [ ] }, { "data": "QualityControl (203)", "attr": { "packageList": "abseqR,AffyExpress,affylmGUI,affyPLM,affyQCReport,AffyRNADegradation,alevinQC,alpine,altcdfenvs,AMARETTO,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,artMS,AssessORF,ATACseqQC,basecallQC,Basic4Cseq,BatchQC,beadarray,bigmelon,bigPint,BioQC,cellity,ChIC,ChIPexoQual,ChIPQC,chipseq,ChromSCape,clstutils,CODEX,CONFESS,consensus,contiBAIT,conumee,countsimQC,CSSP,ctgGEM,cummeRbund,DAPAR,DECIPHER,DegNorm,dexus,diffloop,DiscoRhythm,dks,DMRcate,doppelgangR,Doscheda,dupRadar,dyebias,EDASeq,edgeR,ENmix,erccdashboard,ERSSA,esATAC,farms,FastqCleaner,ffpe,FilterFFPE,flowAI,flowClean,flowCut,gCrisprTools,GENESIS,GladiaTOX,GmicR,Guitar,GWASTools,Harshlight,HELP,hicrep,HTqPCR,iasva,ibh,iCheck,ideal,interactiveDisplay,interactiveDisplayBase,IONiseR,isobar,KnowSeq,limma,limmaGUI,lipidr,lumi,MAGeCKFlute,MANOR,marr,massiR,mdp,mdqc,MEDIPS,metaseqR,metaseqR2,MethylAid,methylumi,minfi,miRcomp,MmPalateMiRNA,monocle,MSnbase,MSstats,MSstatsConvert,MSstatsQC,MSstatsQCgui,MSstatsTMTPTM,MWASTools,NanoStringQCPro,ngsReports,nucleR,OLIN,OLINgui,omicsPrint,Omixer,OSAT,pcaExplorer,PeacoQC,piano,pmp,proBatch,proDA,pRoloc,pvac,qckitfastq,qcmetrics,QDNAseq,qPLEXanalyzer,qrqc,qsea,QuasR,R453Plus1Toolbox,RadioGx,rama,ramwas,RBioinf,RcwlPipelines,recoup,regionReport,REMP,ReQON,Rfastp,RiboProfiling,ribosomeProfilingQC,Ringo,RITAN,RNAinteract,RNAither,rnaseqcomp,RNASeqR,RnBeads,RPA,Rqc,Rsamtools,Rsubread,sangeranalyseR,Scale4C,scater,scBFA,scds,scmeth,scone,SCOPE,scPipe,scruff,scTGIF,scuttle,segmentSeq,seqTools,sesame,shinyMethyl,ShortRead,SICtools,sights,simpleaffy,skewr,SNAGEE,snm,Spaniel,spikeLI,spotSegmentation,Starr,statTarget,strandCheckR,synapter,synlet,systemPipeR,systemPipeShiny,TarSeqQC,TEQC,tidybulk,tidySingleCellExperiment,tidySummarizedExperiment,tRanslatome,traseR,UMI4Cats,unifiedWMWqPCR,variancePartition,wateRmelon,yaqcaffy,yarn", "id": "QualityControl" }, "children": [ ] }, { "data": "ReportWriting (45)", "attr": { "packageList": "abseqR,affycoretools,AffyExpress,annaffy,annmap,arrayQualityMetrics,ArrayTools,biocthis,BiocWorkflowTools,CellScore,ChIPQC,ChromSCape,countsimQC,DEGreport,DMRforPairs,DynDoc,easyreporting,EnrichmentBrowser,GeneTonic,Glimma,GSEABenchmarkeR,Harshlight,ideal,metaseqR,metaseqR2,MmPalateMiRNA,NanoStringQCPro,ngsReports,pcaExplorer,PGA,POMA,qcmetrics,R453Plus1Toolbox,rebook,regionReport,rnaSeqMap,sapFinder,simpleaffy,SpeCond,systemPipeR,systemPipeShiny,tracktables,tximeta,xmapbridge,yaqcaffy", "id": "ReportWriting" }, "children": [ ] }, { "data": "Visualization (506)", "attr": { "packageList": "abseqR,ACE,AffyExpress,alpine,ALPS,AlpsNMR,animalcules,annmap,annotatr,aroma.light,arrayQuality,ArrayTools,ASpediaFI,AssessORF,atSNP,BANDITS,Basic4Cseq,BatchQC,BiGGR,bigPint,bioassayR,bioCancer,biocGraph,BioMVCClass,biomvRCNS,biovizBase,brainflowprobes,BrainSABER,BrowserViz,CAGEfightR,CAGEr,cancerclass,CancerSubtypes,caOmicsV,CATALYST,cellHTS2,cellity,cellscape,CellScore,cellTree,cfDNAPro,CGHcall,CGHregions,ChemmineOB,ChemmineR,ChIPexoQual,ChIPseeker,ChromHeatMap,chromPlot,ChromSCape,clstutils,clustComp,clusterProfiler,CNEr,CNVfilteR,cogena,combi,coMET,compEpiTools,CompGO,ComplexHeatmap,CONFESS,copa,copynumber,CopyNumberPlots,CopywriteR,coRdon,CoRegNet,corral,CountClust,countsimQC,CoverageView,CrispRVariants,CrossICC,ctc,ctgGEM,cummeRbund,cytofast,CytoTree,dagLogo,DECIPHER,DEGreport,deltaGseg,densvis,DepecheR,derfinderPlot,destiny,DEXSeq,DiffLogo,diffloop,Director,DiscoRhythm,distinct,dittoSeq,DMRforPairs,DOSE,drawProteins,Dune,EBImage,ecolitk,eiR,eisa,EnrichedHeatmap,EnrichmentBrowser,enrichplot,epivizr,epivizrChart,epivizrData,epivizrServer,epivizrStandalone,esetVis,explorase,ExpressionView,fabia,FGNet,fishpond,flowcatchR,flowCHIC,flowClust,flowCyBar,flowFP,flowPloidy,flowPlots,FlowSOM,flowSpecs,flowSpy,flowTime,flowViz,fmcsR,focalCall,gaggle,gCrisprTools,GDCRNATools,GeneAnswers,GeneBreak,genefu,GeneOverlap,geneplotter,GeneRegionScan,GeneTonic,geneXtendeR,genomation,GenomicOZone,gespeR,ggbio,ggcyto,ggtree,ggtreeExtra,Glimma,gmoviz,GOexpress,goSTAG,GOsummaries,goTools,GRmetrics,GSCA,GSEABenchmarkeR,GSEAmining,gtrellis,Gviz,GWENA,hapFabia,heatmaps,Heatplus,HELP,HilbertCurve,HilbertVis,HilbertVisGUI,HMMcopy,HPAanalyze,HTqPCR,hyperdraw,ideal,IdeoViz,idiogram,igvR,ILoReg,imageHTS,interactiveDisplay,interactiveDisplayBase,InterMineR,iSEE,iSEEu,IsoformSwitchAnalyzeR,ivygapSE,karyoploteR,KCsmart,KEGGgraph,keggorthology,lipidr,lmdme,Logolas,macat,maCorrPlot,maftools,MAGeCKFlute,mapscape,maser,MassArray,matchBox,mcaGUI,MEDIPS,metagenomeSeq,metavizr,MetCirc,methyAnalysis,MethylAid,Mfuzz,microbiomeDASim,microbiomeExplorer,MicrobiotaProcess,MIGSA,mimager,MineICA,missRows,MOFA,MOFA2,monocle,motifbreakR,motifStack,MSGFgui,MSstatsSampleSize,multiOmicsViz,muscat,MVCClass,NanoMethViz,NarrowPeaks,ncRNAtools,nearBynding,Nebulosa,netbiov,NetSAM,NOISeq,NormalyzerDE,NuPoP,OLIN,OLINgui,OmicCircos,omicplotR,omicRexposome,OMICsPCA,Omixer,oposSOM,OSAT,PANR,PanVizGenerator,PathoStat,pathRender,pathview,PathwaySplice,pcaExplorer,peco,PepsNMR,phantasus,phemd,PhyloProfile,piano,PICS,PING,PloGO2,POMA,prada,proBAMr,pRolocGUI,psichomics,PubScore,Pviz,qcmetrics,qrqc,qsea,quantsmooth,QUBIC,R453Plus1Toolbox,R4RNA,ramwas,Rariant,RCASPAR,rcellminer,RCM,RCy3,RCyjs,RDAVIDWebService,RDRToolbox,ReactomePA,reb,RedeR,regionReport,regutools,ReportingTools,RepViz,rfaRm,RGraph2js,Rgraphviz,riboSeqR,ribosomeProfilingQC,RmiR,RNAinteract,RNAither,RNAmodR,RNAmodR.AlkAnilineSeq,RNAmodR.ML,RNAmodR.RiboMethSeq,rnaseqcomp,rnaSeqMap,RNASeqR,RTCA,rtracklayer,rWikiPathways,sangeranalyseR,sangerseqR,sapFinder,SBGNview,SC3,Scale4C,SCANVIS,scater,scDD,schex,scmap,Sconify,scPipe,scran,scruff,seqcombo,seqPattern,seqplots,seqsetvis,SEtools,SigFuge,sights,signeR,SIM,simpleaffy,simplifyEnrichment,sincell,slalom,slingshot,snifter,SomaticSignatures,Spaniel,sparsenetgls,spatialHeatmap,SplicingGraphs,SPLINTER,splots,SQUADD,ssviz,statTarget,supraHex,survcomp,Sushi,SwimR,synlet,TarSeqQC,TCseq,tilingArray,timescape,TimeSeriesExperiment,TimiRGeN,TnT,tomoda,ToPASeq,topGO,trackViewer,tradeSeq,transcriptogramer,TransView,TreeAndLeaf,tRNA,tRNAdbImport,tRNAscanImport,TSCAN,TVTB,Ularcirc,UMI4Cats,uncoverappLib,unifiedWMWqPCR,vasp,VaSP,vidger,ViSEAGO,wiggleplotr,xmapbridge,YAPSA,yarn", "id": "Visualization" }, "children": [ { "data": "Network (149)", "attr": { "packageList": "ADImpute,AMARETTO,AMOUNTAIN,ANF,ASpediaFI,BayesKnockdown,BiGGR,bioCancer,BioCor,BioNet,BioNetStat,BiRewire,caOmicsV,CARNIVAL,CausalR,CellNOptR,CEMiTool,ceRNAnetsim,CeTF,cliqueMS,CNORfuzzy,coexnet,CoRegFlux,CoRegNet,COSNet,CytoTree,dcanr,DEGraph,DeMAND,DEsubs,diffuStats,DriverNet,EGAD,EGSEA,ELMER,EnrichmentBrowser,epiNEM,fcoex,FELLA,FGNet,flowSpy,GDCRNATools,GENIE3,glmSparseNet,GmicR,GNET2,GOSemSim,GraphAlignment,GraphAT,graphite,GRENITS,GSEABenchmarkeR,gsean,GWENA,IMMAN,Informeasure,interactiveDisplay,interactiveDisplayBase,KEGGlincs,KinSwingR,levi,Linnorm,lionessR,LiquidAssociation,martini,MetaboSignal,MethylMix,MetID,MetNet,minet,mirIntegrator,miRLAB,mnem,MODA,MOGAMUN,MOMA,MoonlightR,ndexr,netbenchmark,netbiov,netboost,netboxr,netDx,NetPathMiner,netprioR,netReg,netresponse,NetSAM,netSmooth,networkBMA,OmnipathR,Onassis,oppti,pageRank,pandaR,Path2PPI,pathifier,PathNet,PathwaySplice,paxtoolsr,PCAN,pcot2,PCpheno,perturbatr,Pi,Pigengene,PoTRA,PPInfer,ppiStats,QUBIC,R3CPET,RandomWalkRestartMH,RBGL,RCy3,RedeR,RegEnrich,regutools,Rgin,RGMQL,RGraph2js,RITAN,rrvgo,rsbml,rScudo,RTN,rTRM,rTRMui,rWikiPathways,SBMLR,SEPIRA,SingleCellSignalR,SLGI,SMITE,spatialHeatmap,SPEM,SpidermiR,SQUADD,StarBioTrek,STRINGdb,TCGAbiolinks,TCGAbiolinksGUI,TimiRGeN,transcriptogramer,transomics2cytoscape,TreeAndLeaf,TRONCO,TxRegInfra,vtpnet,XINA", "id": "Network" }, "children": [ ] } ] } ] } ] }, { "data": "AnnotationData (971)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,AHCytoBands,AHEnsDbs,alternativeSplicingEvents.hg19,alternativeSplicingEvents.hg38,anopheles.db0,arabidopsis.db0,ath1121501.db,ath1121501cdf,ath1121501probe,barley1cdf,barley1probe,bovine.db,bovine.db0,bovinecdf,bovineprobe,BSgenome.Alyrata.JGI.v1,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.NCBI.AmelHAv3.1,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,BSgenome.Aofficinalis.NCBI.V1,BSgenome.Athaliana.TAIR.04232008,BSgenome.Athaliana.TAIR.TAIR9,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.Carietinum.NCBI.v1,BSgenome.Celegans.UCSC.ce10,BSgenome.Celegans.UCSC.ce11,BSgenome.Celegans.UCSC.ce2,BSgenome.Celegans.UCSC.ce6,BSgenome.Cfamiliaris.UCSC.canFam2,BSgenome.Cfamiliaris.UCSC.canFam2.masked,BSgenome.Cfamiliaris.UCSC.canFam3,BSgenome.Cfamiliaris.UCSC.canFam3.masked,BSgenome.Cjacchus.UCSC.calJac3,BSgenome.Creinhardtii.JGI.v5.6,BSgenome.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,BSgenome.Dmelanogaster.UCSC.dm6,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,BSgenome.Dvirilis.Ensembl.dvircaf1,BSgenome.Ecoli.NCBI.20080805,BSgenome.Gaculeatus.UCSC.gasAcu1,BSgenome.Gaculeatus.UCSC.gasAcu1.masked,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,BSgenome.Hsapiens.1000genomes.hs37d5,BSgenome.Hsapiens.NCBI.GRCh38,BSgenome.Hsapiens.UCSC.hg17,BSgenome.Hsapiens.UCSC.hg17.masked,BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg18.masked,BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19.masked,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38.masked,BSgenome.Mdomestica.UCSC.monDom5,BSgenome.Mfascicularis.NCBI.5.0,BSgenome.Mfuro.UCSC.musFur1,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,BSgenome.Mmusculus.UCSC.mm10,BSgenome.Mmusculus.UCSC.mm10.masked,BSgenome.Mmusculus.UCSC.mm8,BSgenome.Mmusculus.UCSC.mm8.masked,BSgenome.Mmusculus.UCSC.mm9,BSgenome.Mmusculus.UCSC.mm9.masked,BSgenome.Osativa.MSU.MSU7,BSgenome.Ppaniscus.UCSC.panPan1,BSgenome.Ppaniscus.UCSC.panPan2,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,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Rnorvegicus.UCSC.rn6,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr11,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tgondii.ToxoDB.7.0,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,BSgenome.Tguttata.UCSC.taeGut2,BSgenome.Vvinifera.URGI.IGGP12Xv0,BSgenome.Vvinifera.URGI.IGGP12Xv2,BSgenome.Vvinifera.URGI.IGGP8X,bsubtiliscdf,bsubtilisprobe,canine.db,canine.db0,canine2.db,canine2cdf,canine2probe,caninecdf,canineprobe,celegans.db,celeganscdf,celegansprobe,ChemmineDrugs,chicken.db,chicken.db0,chickencdf,chickenprobe,chimp.db0,citruscdf,citrusprobe,clariomdhumanprobeset.db,clariomdhumantranscriptcluster.db,clariomshumanhttranscriptcluster.db,clariomshumantranscriptcluster.db,clariomsmousehttranscriptcluster.db,clariomsmousetranscriptcluster.db,clariomsrathttranscriptcluster.db,clariomsrattranscriptcluster.db,cMAP,cottoncdf,cottonprobe,cyp450cdf,DO.db,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliK12.db0,ecoliprobe,ecoliSakai.db0,ENCODExplorerData,EnsDb.Hsapiens.v75,EnsDb.Hsapiens.v79,EnsDb.Hsapiens.v86,EnsDb.Mmusculus.v75,EnsDb.Mmusculus.v79,EnsDb.Rnorvegicus.v75,EnsDb.Rnorvegicus.v79,EpiTxDb.Hs.hg38,EpiTxDb.Mm.mm10,EpiTxDb.Sc.sacCer3,EuPathDB,FDb.FANTOM4.promoters.hg19,FDb.InfiniumMethylation.hg18,FDb.InfiniumMethylation.hg19,FDb.UCSC.snp135common.hg19,FDb.UCSC.snp137common.hg19,FDb.UCSC.tRNAs,fitCons.UCSC.hg19,fly.db0,geneplast.data,geneplast.data.string.v91,GenomeInfoDbData,genomewidesnp5Crlmm,genomewidesnp6Crlmm,GenomicState,GGHumanMethCancerPanelv1.db,GO.db,gp53cdf,grasp2db,greengenes13.5MgDb,h10kcod.db,h20kcod.db,hapmap370k,hcg110.db,hcg110cdf,hcg110probe,hgfocus.db,hgfocuscdf,hgfocusprobe,hgu133a.db,hgu133a2.db,hgu133a2cdf,hgu133a2frmavecs,hgu133a2probe,hgu133acdf,hgu133afrmavecs,hgu133aprobe,hgu133atagcdf,hgu133atagprobe,hgu133b.db,hgu133bcdf,hgu133bprobe,hgu133plus2.db,hgu133plus2cdf,hgu133plus2frmavecs,hgu133plus2probe,hgu219.db,hgu219cdf,hgu219probe,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,hgubeta7.db,hguDKFZ31.db,hgug4100a.db,hgug4101a.db,hgug4110b.db,hgug4111a.db,hgug4112a.db,hgug4845a.db,hguqiagenv3.db,hi16cod.db,hivprtplus2cdf,hom.At.inp.db,hom.Ce.inp.db,hom.Dm.inp.db,hom.Dr.inp.db,hom.Hs.inp.db,hom.Mm.inp.db,hom.Rn.inp.db,hom.Sc.inp.db,Homo.sapiens,hpAnnot,hs25kresogen.db,Hs6UG171.db,HsAgilentDesign026652.db,Hspec,hspeccdf,hta20probeset.db,hta20transcriptcluster.db,hthgu133a.db,hthgu133acdf,hthgu133afrmavecs,hthgu133aprobe,hthgu133b.db,hthgu133bcdf,hthgu133bprobe,hthgu133pluspmcdf,hthgu133pluspmprobe,htmg430acdf,htmg430aprobe,htmg430bcdf,htmg430bprobe,htmg430pmcdf,htmg430pmprobe,htrat230pmcdf,htrat230pmprobe,htratfocuscdf,htratfocusprobe,hu35ksuba.db,hu35ksubacdf,hu35ksubaprobe,hu35ksubb.db,hu35ksubbcdf,hu35ksubbprobe,hu35ksubc.db,hu35ksubccdf,hu35ksubcprobe,hu35ksubd.db,hu35ksubdcdf,hu35ksubdprobe,hu6800.db,hu6800cdf,hu6800probe,hu6800subacdf,hu6800subbcdf,hu6800subccdf,hu6800subdcdf,huex.1.0.st.v2frmavecs,huex10stprobeset.db,huex10sttranscriptcluster.db,HuExExonProbesetLocation,HuExExonProbesetLocationHg18,HuExExonProbesetLocationHg19,hugene.1.0.st.v1frmavecs,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene10stv1cdf,hugene10stv1probe,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,human.db0,human1mduov3bCrlmm,human1mv1cCrlmm,human370quadv3cCrlmm,human370v1cCrlmm,human550v3bCrlmm,human610quadv1bCrlmm,human650v3aCrlmm,human660quadv1aCrlmm,humanCHRLOC,humancytosnp12v2p1hCrlmm,humanomni1quadv1bCrlmm,humanomni25quadv1bCrlmm,humanomni5quadv1bCrlmm,humanomniexpress12v1bCrlmm,HuO22.db,hwgcod.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kanno.ilmn12.hg19,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylation450kprobe,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,IlluminaHumanMethylationEPICanno.ilm10b3.hg19,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,IlluminaHumanMethylationEPICmanifest,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,illuminaMousev1.db,illuminaMousev1p1.db,illuminaMousev2.db,illuminaRatv1.db,indac.db,JASPAR2018,JASPAR2020,JazaeriMetaData.db,KEGG.db,LAPOINTE.db,LowMACAAnnotation,LRBase.Ath.eg.db,LRBase.Bta.eg.db,LRBase.Cel.eg.db,LRBase.Dme.eg.db,LRBase.Dre.eg.db,LRBase.Gga.eg.db,LRBase.Hsa.eg.db,LRBase.Mmu.eg.db,LRBase.Pab.eg.db,LRBase.Rno.eg.db,LRBase.Ssc.eg.db,LRBase.Xtr.eg.db,lumiHumanAll.db,lumiHumanIDMapping,lumiMouseAll.db,lumiMouseIDMapping,lumiRatAll.db,lumiRatIDMapping,LymphoSeqDB,m10kcod.db,m20kcod.db,MafDb.1Kgenomes.phase1.GRCh38,MafDb.1Kgenomes.phase1.hs37d5,MafDb.1Kgenomes.phase3.GRCh38,MafDb.1Kgenomes.phase3.hs37d5,MafDb.ExAC.r1.0.GRCh38,MafDb.ExAC.r1.0.hs37d5,MafDb.ExAC.r1.0.nonTCGA.GRCh38,MafDb.ExAC.r1.0.nonTCGA.hs37d5,MafDb.gnomAD.r2.1.GRCh38,MafDb.gnomAD.r2.1.hs37d5,MafDb.gnomAD.r3.0.GRCh38,MafDb.gnomADex.r2.1.GRCh38,MafDb.gnomADex.r2.1.hs37d5,MafDb.TOPMed.freeze5.hg19,MafDb.TOPMed.freeze5.hg38,MafH5.gnomAD.r3.0.GRCh38,maizecdf,maizeprobe,malaria.db0,medicagocdf,medicagoprobe,MeSH.Aca.eg.db,MeSH.Aga.PEST.eg.db,MeSH.Ame.eg.db,MeSH.Aml.eg.db,MeSH.Ana.eg.db,MeSH.Ani.FGSC.eg.db,MeSH.AOR.db,MeSH.Ath.eg.db,MeSH.Bfl.eg.db,MeSH.Bsu.168.eg.db,MeSH.Bta.eg.db,MeSH.Cal.SC5314.eg.db,MeSH.Cbr.eg.db,MeSH.Cel.eg.db,MeSH.Cfa.eg.db,MeSH.Cin.eg.db,MeSH.Cja.eg.db,MeSH.Cpo.eg.db,MeSH.Cre.eg.db,MeSH.Dan.eg.db,MeSH.db,MeSH.Dda.3937.eg.db,MeSH.Ddi.AX4.eg.db,MeSH.Der.eg.db,MeSH.Dgr.eg.db,MeSH.Dme.eg.db,MeSH.Dmo.eg.db,MeSH.Dpe.eg.db,MeSH.Dre.eg.db,MeSH.Dse.eg.db,MeSH.Dsi.eg.db,MeSH.Dvi.eg.db,MeSH.Dya.eg.db,MeSH.Eca.eg.db,MeSH.Eco.55989.eg.db,MeSH.Eco.ED1a.eg.db,MeSH.Eco.IAI39.eg.db,MeSH.Eco.K12.MG1655.eg.db,MeSH.Eco.O157.H7.Sakai.eg.db,MeSH.Eco.UMN026.eg.db,MeSH.Eqc.eg.db,MeSH.Gga.eg.db,MeSH.Gma.eg.db,MeSH.Hsa.eg.db,MeSH.Laf.eg.db,MeSH.Lma.eg.db,MeSH.Mdo.eg.db,MeSH.Mes.eg.db,MeSH.Mga.eg.db,MeSH.Miy.eg.db,MeSH.Mml.eg.db,MeSH.Mmu.eg.db,MeSH.Mtr.eg.db,MeSH.Nle.eg.db,MeSH.Oan.eg.db,MeSH.Ocu.eg.db,MeSH.Oni.eg.db,MeSH.Osa.eg.db,MeSH.Pab.eg.db,MeSH.Pae.PAO1.eg.db,MeSH.PCR.db,MeSH.Pfa.3D7.eg.db,MeSH.Pto.eg.db,MeSH.Ptr.eg.db,MeSH.Rno.eg.db,MeSH.Sce.S288c.eg.db,MeSH.Sco.A32.eg.db,MeSH.Sil.eg.db,MeSH.Spu.eg.db,MeSH.Ssc.eg.db,MeSH.Syn.eg.db,MeSH.Tbr.9274.eg.db,MeSH.Tgo.ME49.eg.db,MeSH.Tgu.eg.db,MeSH.Vvi.eg.db,MeSH.Xla.eg.db,MeSH.Xtr.eg.db,MeSH.Zma.eg.db,metaboliteIDmapping,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,mirbase.db,miRBaseVersions.db,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,miRNAtap.db,mm24kresogen.db,MmAgilentDesign026655.db,moe430a.db,moe430acdf,moe430aprobe,moe430b.db,moe430bcdf,moe430bprobe,moex10stprobeset.db,moex10sttranscriptcluster.db,MoExExonProbesetLocation,mogene.1.0.st.v1frmavecs,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,Norway981.db,nugohs1a520180.db,nugohs1a520180cdf,nugohs1a520180probe,nugomm1a520177.db,nugomm1a520177cdf,nugomm1a520177probe,oligoData,OperonHumanV3.db,org.Ag.eg.db,org.At.tair.db,org.Bt.eg.db,org.Ce.eg.db,org.Cf.eg.db,org.Dm.eg.db,org.Dr.eg.db,org.EcK12.eg.db,org.EcSakai.eg.db,org.Gg.eg.db,org.Hs.eg.db,org.Mm.eg.db,org.Mmu.eg.db,org.Mxanthus.db,org.Pf.plasmo.db,org.Pt.eg.db,org.Rn.eg.db,org.Sc.sgd.db,org.Ss.eg.db,org.Xl.eg.db,paeg1acdf,paeg1aprobe,PANTHER.db,PartheenMetaData.db,pd.081229.hg18.promoter.medip.hx1,pd.2006.07.18.hg18.refseq.promoter,pd.2006.07.18.mm8.refseq.promoter,pd.2006.10.31.rn34.refseq.promoter,pd.ag,pd.aragene.1.0.st,pd.aragene.1.1.st,pd.ath1.121501,pd.barley1,pd.bovgene.1.0.st,pd.bovgene.1.1.st,pd.bovine,pd.bsubtilis,pd.cangene.1.0.st,pd.cangene.1.1.st,pd.canine,pd.canine.2,pd.celegans,pd.charm.hg18.example,pd.chicken,pd.chigene.1.0.st,pd.chigene.1.1.st,pd.chogene.2.0.st,pd.chogene.2.1.st,pd.citrus,pd.clariom.d.human,pd.clariom.s.human,pd.clariom.s.human.ht,pd.clariom.s.mouse,pd.clariom.s.mouse.ht,pd.clariom.s.rat,pd.clariom.s.rat.ht,pd.cotton,pd.cyngene.1.0.st,pd.cyngene.1.1.st,pd.cyrgene.1.0.st,pd.cyrgene.1.1.st,pd.cytogenetics.array,pd.drogene.1.0.st,pd.drogene.1.1.st,pd.drosgenome1,pd.drosophila.2,pd.e.coli.2,pd.ecoli,pd.ecoli.asv2,pd.elegene.1.0.st,pd.elegene.1.1.st,pd.equgene.1.0.st,pd.equgene.1.1.st,pd.feinberg.hg18.me.hx1,pd.feinberg.mm8.me.hx1,pd.felgene.1.0.st,pd.felgene.1.1.st,pd.fingene.1.0.st,pd.fingene.1.1.st,pd.genomewidesnp.5,pd.genomewidesnp.6,pd.guigene.1.0.st,pd.guigene.1.1.st,pd.hc.g110,pd.hg.focus,pd.hg.u133.plus.2,pd.hg.u133a,pd.hg.u133a.2,pd.hg.u133a.tag,pd.hg.u133b,pd.hg.u219,pd.hg.u95a,pd.hg.u95av2,pd.hg.u95b,pd.hg.u95c,pd.hg.u95d,pd.hg.u95e,pd.hg18.60mer.expr,pd.ht.hg.u133.plus.pm,pd.ht.hg.u133a,pd.ht.mg.430a,pd.hta.2.0,pd.hu6800,pd.huex.1.0.st.v2,pd.hugene.1.0.st.v1,pd.hugene.1.1.st.v1,pd.hugene.2.0.st,pd.hugene.2.1.st,pd.maize,pd.mapping250k.nsp,pd.mapping250k.sty,pd.mapping50k.hind240,pd.mapping50k.xba240,pd.margene.1.0.st,pd.margene.1.1.st,pd.medgene.1.0.st,pd.medgene.1.1.st,pd.medicago,pd.mg.u74a,pd.mg.u74av2,pd.mg.u74b,pd.mg.u74bv2,pd.mg.u74c,pd.mg.u74cv2,pd.mirna.1.0,pd.mirna.2.0,pd.mirna.3.0,pd.mirna.3.1,pd.mirna.4.0,pd.moe430a,pd.moe430b,pd.moex.1.0.st.v1,pd.mogene.1.0.st.v1,pd.mogene.1.1.st.v1,pd.mogene.2.0.st,pd.mogene.2.1.st,pd.mouse430.2,pd.mouse430a.2,pd.mta.1.0,pd.mu11ksuba,pd.mu11ksubb,pd.nugo.hs1a520180,pd.nugo.mm1a520177,pd.ovigene.1.0.st,pd.ovigene.1.1.st,pd.pae.g1a,pd.plasmodium.anopheles,pd.poplar,pd.porcine,pd.porgene.1.0.st,pd.porgene.1.1.st,pd.rabgene.1.0.st,pd.rabgene.1.1.st,pd.rae230a,pd.rae230b,pd.raex.1.0.st.v1,pd.ragene.1.0.st.v1,pd.ragene.1.1.st.v1,pd.ragene.2.0.st,pd.ragene.2.1.st,pd.rat230.2,pd.rcngene.1.0.st,pd.rcngene.1.1.st,pd.rg.u34a,pd.rg.u34b,pd.rg.u34c,pd.rhegene.1.0.st,pd.rhegene.1.1.st,pd.rhesus,pd.rice,pd.rjpgene.1.0.st,pd.rjpgene.1.1.st,pd.rn.u34,pd.rta.1.0,pd.rusgene.1.0.st,pd.rusgene.1.1.st,pd.s.aureus,pd.soybean,pd.soygene.1.0.st,pd.soygene.1.1.st,pd.sugar.cane,pd.tomato,pd.u133.x3p,pd.vitis.vinifera,pd.wheat,pd.x.laevis.2,pd.x.tropicalis,pd.xenopus.laevis,pd.yeast.2,pd.yg.s98,pd.zebgene.1.0.st,pd.zebgene.1.1.st,pd.zebrafish,pedbarrayv10.db,pedbarrayv9.db,PFAM.db,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons30way.UCSC.hg38,phastCons7way.UCSC.hg38,pig.db0,plasmodiumanophelescdf,plasmodiumanophelesprobe,POCRCannotation.db,PolyPhen.Hsapiens.dbSNP131,poplarcdf,poplarprobe,porcine.db,porcinecdf,porcineprobe,primeviewcdf,primeviewprobe,r10kcod.db,rae230a.db,rae230acdf,rae230aprobe,rae230b.db,rae230bcdf,rae230bprobe,raex10stprobeset.db,raex10sttranscriptcluster.db,RaExExonProbesetLocation,ragene10stprobeset.db,ragene10sttranscriptcluster.db,ragene10stv1cdf,ragene10stv1probe,ragene11stprobeset.db,ragene11sttranscriptcluster.db,ragene20stprobeset.db,ragene20sttranscriptcluster.db,ragene21stprobeset.db,ragene21sttranscriptcluster.db,rat.db0,rat2302.db,rat2302cdf,rat2302frmavecs,rat2302probe,ratCHRLOC,rattoxfxcdf,rattoxfxprobe,Rattus.norvegicus,reactome.db,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rguatlas4k.db,rgug4105a.db,rgug4130a.db,rgug4131a.db,rhesus.db0,rhesuscdf,rhesusprobe,ri16cod.db,ribosomaldatabaseproject11.5MgDb,ricecdf,riceprobe,RmiR.Hs.miRNA,RmiR.hsa,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,Roberts2005Annotation.db,rta10probeset.db,rta10transcriptcluster.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,saureuscdf,saureusprobe,SHDZ.db,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,silva128.1MgDb,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP142.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP151.GRCh38,soybeancdf,soybeanprobe,sugarcanecdf,sugarcaneprobe,targetscan.Hs.eg.db,targetscan.Mm.eg.db,test1cdf,test2cdf,test3cdf,test3probe,tomatocdf,tomatoprobe,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Athaliana.BioMart.plantsmart25,TxDb.Athaliana.BioMart.plantsmart28,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.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.hg38.knownGene,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.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.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,TxDb.Sscrofa.UCSC.susScr11.refGene,TxDb.Sscrofa.UCSC.susScr3.refGene,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,wheatcdf,wheatprobe,worm.db0,xenopus.db0,xenopuslaeviscdf,xenopuslaevisprobe,xlaevis.db,xlaevis2cdf,xlaevis2probe,XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38,xtropicaliscdf,xtropicalisprobe,ye6100subacdf,ye6100subbcdf,ye6100subccdf,ye6100subdcdf,yeast.db0,yeast2.db,yeast2cdf,yeast2probe,ygs98.db,ygs98cdf,ygs98frmavecs,ygs98probe,zebrafish.db,zebrafish.db0,zebrafishcdf,zebrafishprobe", "id": "AnnotationData" }, "children": [ { "data": "ChipManufacturer (388)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,ath1121501.db,ath1121501cdf,ath1121501probe,barley1cdf,barley1probe,bovine.db,bovinecdf,bovineprobe,bsubtiliscdf,bsubtilisprobe,canine.db,canine2.db,canine2cdf,canine2probe,caninecdf,canineprobe,celegans.db,celeganscdf,celegansprobe,chicken.db,chickencdf,chickenprobe,citruscdf,citrusprobe,clariomdhumanprobeset.db,clariomdhumantranscriptcluster.db,clariomshumanhttranscriptcluster.db,clariomshumantranscriptcluster.db,clariomsmousehttranscriptcluster.db,clariomsmousetranscriptcluster.db,clariomsrathttranscriptcluster.db,clariomsrattranscriptcluster.db,cottoncdf,cottonprobe,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliprobe,GGHumanMethCancerPanelv1.db,gp53cdf,h10kcod.db,h20kcod.db,hcg110.db,hcg110cdf,hcg110probe,hgfocus.db,hgfocuscdf,hgfocusprobe,hgu133a.db,hgu133a2.db,hgu133a2cdf,hgu133a2frmavecs,hgu133a2probe,hgu133acdf,hgu133afrmavecs,hgu133aprobe,hgu133atagcdf,hgu133atagprobe,hgu133b.db,hgu133bcdf,hgu133bprobe,hgu133plus2.db,hgu133plus2cdf,hgu133plus2frmavecs,hgu133plus2probe,hgu219.db,hgu219cdf,hgu219probe,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,hgug4100a.db,hgug4101a.db,hgug4110b.db,hgug4111a.db,hgug4112a.db,hguqiagenv3.db,hi16cod.db,hivprtplus2cdf,hs25kresogen.db,HsAgilentDesign026652.db,Hspec,hspeccdf,hta20probeset.db,hta20transcriptcluster.db,hthgu133a.db,hthgu133acdf,hthgu133afrmavecs,hthgu133aprobe,hthgu133b.db,hthgu133bcdf,hthgu133bprobe,hthgu133pluspmcdf,hthgu133pluspmprobe,htmg430acdf,htmg430aprobe,htmg430bcdf,htmg430bprobe,htmg430pmcdf,htmg430pmprobe,htrat230pmcdf,htrat230pmprobe,htratfocuscdf,htratfocusprobe,hu35ksuba.db,hu35ksubacdf,hu35ksubaprobe,hu35ksubb.db,hu35ksubbcdf,hu35ksubbprobe,hu35ksubc.db,hu35ksubccdf,hu35ksubcprobe,hu35ksubd.db,hu35ksubdcdf,hu35ksubdprobe,hu6800.db,hu6800cdf,hu6800probe,hu6800subacdf,hu6800subbcdf,hu6800subccdf,hu6800subdcdf,huex.1.0.st.v2frmavecs,huex10stprobeset.db,huex10sttranscriptcluster.db,HuExExonProbesetLocation,HuExExonProbesetLocationHg18,HuExExonProbesetLocationHg19,hugene.1.0.st.v1frmavecs,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene10stv1cdf,hugene10stv1probe,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,hwgcod.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kanno.ilmn12.hg19,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,IlluminaHumanMethylationEPICanno.ilm10b3.hg19,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,IlluminaHumanMethylationEPICmanifest,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,illuminaMousev1.db,illuminaMousev1p1.db,illuminaMousev2.db,illuminaRatv1.db,indac.db,lumiHumanAll.db,lumiMouseAll.db,lumiRatAll.db,m10kcod.db,m20kcod.db,maizecdf,maizeprobe,medicagocdf,medicagoprobe,mgu74a.db,mgu74acdf,mgu74aprobe,mgu74av2.db,mgu74av2cdf,mgu74av2probe,mgu74b.db,mgu74bcdf,mgu74bprobe,mgu74bv2.db,mgu74bv2cdf,mgu74bv2probe,mgu74c.db,mgu74ccdf,mgu74cprobe,mgu74cv2.db,mgu74cv2cdf,mgu74cv2probe,mgug4104a.db,mgug4120a.db,mgug4121a.db,mgug4122a.db,mi16cod.db,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,mm24kresogen.db,MmAgilentDesign026655.db,moe430a.db,moe430acdf,moe430aprobe,moe430b.db,moe430bcdf,moe430bprobe,moex10stprobeset.db,moex10sttranscriptcluster.db,MoExExonProbesetLocation,mogene.1.0.st.v1frmavecs,mogene10stprobeset.db,mogene10sttranscriptcluster.db,mogene10stv1cdf,mogene10stv1probe,mogene11stprobeset.db,mogene11sttranscriptcluster.db,mogene20stprobeset.db,mogene20sttranscriptcluster.db,mogene21stprobeset.db,mogene21sttranscriptcluster.db,mouse4302.db,mouse4302cdf,mouse4302frmavecs,mouse4302probe,mouse430a2.db,mouse430a2cdf,mouse430a2frmavecs,mouse430a2probe,mta10probeset.db,mta10transcriptcluster.db,mu11ksuba.db,mu11ksubacdf,mu11ksubaprobe,mu11ksubb.db,mu11ksubbcdf,mu11ksubbprobe,mu19ksuba.db,mu19ksubacdf,mu19ksubb.db,mu19ksubbcdf,mu19ksubc.db,mu19ksubccdf,mu6500subacdf,mu6500subbcdf,mu6500subccdf,mu6500subdcdf,mwgcod.db,nugohs1a520180.db,nugohs1a520180cdf,nugohs1a520180probe,nugomm1a520177.db,nugomm1a520177cdf,nugomm1a520177probe,paeg1acdf,paeg1aprobe,plasmodiumanophelescdf,plasmodiumanophelesprobe,poplarcdf,poplarprobe,porcine.db,porcinecdf,porcineprobe,primeviewcdf,primeviewprobe,r10kcod.db,rae230a.db,rae230acdf,rae230aprobe,rae230b.db,rae230bcdf,rae230bprobe,raex10stprobeset.db,raex10sttranscriptcluster.db,RaExExonProbesetLocation,ragene10stprobeset.db,ragene10sttranscriptcluster.db,ragene10stv1cdf,ragene10stv1probe,ragene11stprobeset.db,ragene11sttranscriptcluster.db,ragene20stprobeset.db,ragene20sttranscriptcluster.db,ragene21stprobeset.db,ragene21sttranscriptcluster.db,rat2302.db,rat2302cdf,rat2302frmavecs,rat2302probe,rattoxfxcdf,rattoxfxprobe,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rgug4105a.db,rgug4130a.db,rgug4131a.db,rhesuscdf,rhesusprobe,ri16cod.db,ricecdf,riceprobe,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,rta10probeset.db,rta10transcriptcluster.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,saureuscdf,saureusprobe,soybeancdf,soybeanprobe,sugarcanecdf,sugarcaneprobe,test1cdf,test2cdf,test3cdf,test3probe,tomatocdf,tomatoprobe,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,wheatcdf,wheatprobe,xenopuslaeviscdf,xenopuslaevisprobe,xlaevis.db,xlaevis2cdf,xlaevis2probe,xtropicaliscdf,xtropicalisprobe,ye6100subacdf,ye6100subbcdf,ye6100subccdf,ye6100subdcdf,yeast2.db,yeast2cdf,yeast2probe,ygs98.db,ygs98cdf,ygs98frmavecs,ygs98probe,zebrafish.db,zebrafishcdf,zebrafishprobe", "id": "ChipManufacturer" }, "children": [ { "data": "AffymetrixChip (333)", "attr": { "packageList": "ag.db,agcdf,agprobe,ath1121501.db,ath1121501cdf,ath1121501probe,barley1cdf,barley1probe,bovine.db,bovinecdf,bovineprobe,bsubtiliscdf,bsubtilisprobe,canine.db,canine2.db,canine2cdf,canine2probe,caninecdf,canineprobe,celegans.db,celeganscdf,celegansprobe,chicken.db,chickencdf,chickenprobe,citruscdf,citrusprobe,clariomdhumanprobeset.db,clariomdhumantranscriptcluster.db,clariomshumanhttranscriptcluster.db,clariomshumantranscriptcluster.db,clariomsmousehttranscriptcluster.db,clariomsmousetranscriptcluster.db,clariomsrathttranscriptcluster.db,clariomsrattranscriptcluster.db,cottoncdf,cottonprobe,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliprobe,gp53cdf,hcg110.db,hcg110cdf,hcg110probe,hgfocus.db,hgfocuscdf,hgfocusprobe,hgu133a.db,hgu133a2.db,hgu133a2cdf,hgu133a2frmavecs,hgu133a2probe,hgu133acdf,hgu133afrmavecs,hgu133aprobe,hgu133atagcdf,hgu133atagprobe,hgu133b.db,hgu133bcdf,hgu133bprobe,hgu133plus2.db,hgu133plus2cdf,hgu133plus2frmavecs,hgu133plus2probe,hgu219.db,hgu219cdf,hgu219probe,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,hivprtplus2cdf,Hspec,hspeccdf,hta20probeset.db,hta20transcriptcluster.db,hthgu133a.db,hthgu133acdf,hthgu133afrmavecs,hthgu133aprobe,hthgu133b.db,hthgu133bcdf,hthgu133bprobe,hthgu133pluspmcdf,hthgu133pluspmprobe,htmg430acdf,htmg430aprobe,htmg430bcdf,htmg430bprobe,htmg430pmcdf,htmg430pmprobe,htrat230pmcdf,htrat230pmprobe,htratfocuscdf,htratfocusprobe,hu35ksuba.db,hu35ksubacdf,hu35ksubaprobe,hu35ksubb.db,hu35ksubbcdf,hu35ksubbprobe,hu35ksubc.db,hu35ksubccdf,hu35ksubcprobe,hu35ksubd.db,hu35ksubdcdf,hu35ksubdprobe,hu6800.db,hu6800cdf,hu6800probe,hu6800subacdf,hu6800subbcdf,hu6800subccdf,hu6800subdcdf,huex.1.0.st.v2frmavecs,huex10stprobeset.db,huex10sttranscriptcluster.db,HuExExonProbesetLocation,HuExExonProbesetLocationHg18,HuExExonProbesetLocationHg19,hugene.1.0.st.v1frmavecs,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene10stv1cdf,hugene10stv1probe,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,maizecdf,maizeprobe,medicagocdf,medicagoprobe,mgu74a.db,mgu74acdf,mgu74aprobe,mgu74av2.db,mgu74av2cdf,mgu74av2probe,mgu74b.db,mgu74bcdf,mgu74bprobe,mgu74bv2.db,mgu74bv2cdf,mgu74bv2probe,mgu74c.db,mgu74ccdf,mgu74cprobe,mgu74cv2.db,mgu74cv2cdf,mgu74cv2probe,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,moe430a.db,moe430acdf,moe430aprobe,moe430b.db,moe430bcdf,moe430bprobe,moex10stprobeset.db,moex10sttranscriptcluster.db,MoExExonProbesetLocation,mogene.1.0.st.v1frmavecs,mogene10stprobeset.db,mogene10sttranscriptcluster.db,mogene10stv1cdf,mogene10stv1probe,mogene11stprobeset.db,mogene11sttranscriptcluster.db,mogene20stprobeset.db,mogene20sttranscriptcluster.db,mogene21stprobeset.db,mogene21sttranscriptcluster.db,mouse4302.db,mouse4302cdf,mouse4302frmavecs,mouse4302probe,mouse430a2.db,mouse430a2cdf,mouse430a2frmavecs,mouse430a2probe,mta10probeset.db,mta10transcriptcluster.db,mu11ksuba.db,mu11ksubacdf,mu11ksubaprobe,mu11ksubb.db,mu11ksubbcdf,mu11ksubbprobe,mu19ksuba.db,mu19ksubacdf,mu19ksubb.db,mu19ksubbcdf,mu19ksubc.db,mu19ksubccdf,mu6500subacdf,mu6500subbcdf,mu6500subccdf,mu6500subdcdf,nugohs1a520180.db,nugohs1a520180cdf,nugohs1a520180probe,nugomm1a520177.db,nugomm1a520177cdf,nugomm1a520177probe,paeg1acdf,paeg1aprobe,plasmodiumanophelescdf,plasmodiumanophelesprobe,poplarcdf,poplarprobe,porcine.db,porcinecdf,porcineprobe,primeviewcdf,primeviewprobe,rae230a.db,rae230acdf,rae230aprobe,rae230b.db,rae230bcdf,rae230bprobe,raex10stprobeset.db,raex10sttranscriptcluster.db,RaExExonProbesetLocation,ragene10stprobeset.db,ragene10sttranscriptcluster.db,ragene10stv1cdf,ragene10stv1probe,ragene11stprobeset.db,ragene11sttranscriptcluster.db,ragene20stprobeset.db,ragene20sttranscriptcluster.db,ragene21stprobeset.db,ragene21sttranscriptcluster.db,rat2302.db,rat2302cdf,rat2302frmavecs,rat2302probe,rattoxfxcdf,rattoxfxprobe,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rhesuscdf,rhesusprobe,ricecdf,riceprobe,rnu34.db,rnu34cdf,rnu34probe,rta10probeset.db,rta10transcriptcluster.db,rtu34.db,rtu34cdf,rtu34probe,saureuscdf,saureusprobe,soybeancdf,soybeanprobe,sugarcanecdf,sugarcaneprobe,test1cdf,test2cdf,test3cdf,test3probe,tomatocdf,tomatoprobe,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,wheatcdf,wheatprobe,xenopuslaeviscdf,xenopuslaevisprobe,xlaevis.db,xlaevis2cdf,xlaevis2probe,xtropicaliscdf,xtropicalisprobe,ye6100subacdf,ye6100subbcdf,ye6100subccdf,ye6100subdcdf,yeast2.db,yeast2cdf,yeast2probe,ygs98.db,ygs98cdf,ygs98frmavecs,ygs98probe,zebrafish.db,zebrafishcdf,zebrafishprobe", "id": "AffymetrixChip" }, "children": [ ] }, { "data": "AgilentChip (15)", "attr": { "packageList": "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", "id": "AgilentChip" }, "children": [ ] }, { "childnum": 0, "data": "ClonetechChip", "children": [ ] }, { "data": "CodelinkChip (12)", "attr": { "packageList": "adme16cod.db,h10kcod.db,h20kcod.db,hi16cod.db,hwgcod.db,m10kcod.db,m20kcod.db,mi16cod.db,mwgcod.db,r10kcod.db,ri16cod.db,rwgcod.db", "id": "CodelinkChip" }, "children": [ ] }, { "childnum": 0, "data": "GEChip", "children": [ ] }, { "data": "IlluminaChip (24)", "attr": { "packageList": "GGHumanMethCancerPanelv1.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kanno.ilmn12.hg19,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,IlluminaHumanMethylationEPICanno.ilm10b3.hg19,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,IlluminaHumanMethylationEPICmanifest,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,illuminaMousev1.db,illuminaMousev1p1.db,illuminaMousev2.db,illuminaRatv1.db,lumiHumanAll.db,lumiMouseAll.db,lumiRatAll.db", "id": "IlluminaChip" }, "children": [ ] }, { "data": "INDACChip (1)", "attr": { "packageList": "indac.db", "id": "INDACChip" }, "children": [ ] }, { "data": "QiagenChip (1)", "attr": { "packageList": "hguqiagenv3.db", "id": "QiagenChip" }, "children": [ ] }, { "data": "RNG_MRCChip (2)", "attr": { "packageList": "hs25kresogen.db,mm24kresogen.db", "id": "RNG_MRCChip" }, "children": [ ] }, { "childnum": 0, "data": "RocheChip", "children": [ ] }, { "childnum": 0, "data": "UniversityHealthNetwork", "children": [ ] } ] }, { "data": "ChipName (196)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,ath1121501.db,ath1121501cdf,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", "id": "ChipName" }, "children": [ { "data": "adme16cod (1)", "attr": { "packageList": "adme16cod.db", "id": "adme16cod" }, "children": [ ] }, { "data": "ag (3)", "attr": { "packageList": "ag.db,agcdf,agprobe", "id": "ag" }, "children": [ ] }, { "data": "ath1121501 (3)", "attr": { "packageList": "ath1121501.db,ath1121501cdf,ath1121501probe", "id": "ath1121501" }, "children": [ ] }, { "data": "celegans (3)", "attr": { "packageList": "celegans.db,celeganscdf,celegansprobe", "id": "celegans" }, "children": [ ] }, { "data": "drosgenome1 (3)", "attr": { "packageList": "drosgenome1.db,drosgenome1cdf,drosgenome1probe", "id": "drosgenome1" }, "children": [ ] }, { "data": "drosophila2 (3)", "attr": { "packageList": "drosophila2.db,drosophila2cdf,drosophila2probe", "id": "drosophila2" }, "children": [ ] }, { "data": "h10kcod (1)", "attr": { "packageList": "h10kcod.db", "id": "h10kcod" }, "children": [ ] }, { "data": "h20kcod (1)", "attr": { "packageList": "h20kcod.db", "id": "h20kcod" }, "children": [ ] }, { "data": "hcg110 (3)", "attr": { "packageList": "hcg110.db,hcg110cdf,hcg110probe", "id": "hcg110" }, "children": [ ] }, { "childnum": 0, "data": "hcgi12k", "children": [ ] }, { "childnum": 0, "data": "hcgi8k", "children": [ ] }, { "data": "hgfocus (3)", "attr": { "packageList": "hgfocus.db,hgfocuscdf,hgfocusprobe", "id": "hgfocus" }, "children": [ ] }, { "data": "hgu133a (4)", "attr": { "packageList": "hgu133a.db,hgu133acdf,hgu133afrmavecs,hgu133aprobe", "id": "hgu133a" }, "children": [ ] }, { "data": "hgu133a2 (4)", "attr": { "packageList": "hgu133a2.db,hgu133a2cdf,hgu133a2frmavecs,hgu133a2probe", "id": "hgu133a2" }, "children": [ ] }, { "data": "hgu133b (3)", "attr": { "packageList": "hgu133b.db,hgu133bcdf,hgu133bprobe", "id": "hgu133b" }, "children": [ ] }, { "data": "hgu133plus2 (4)", "attr": { "packageList": "hgu133plus2.db,hgu133plus2cdf,hgu133plus2frmavecs,hgu133plus2probe", "id": "hgu133plus2" }, "children": [ ] }, { "data": "hgu95a (3)", "attr": { "packageList": "hgu95a.db,hgu95acdf,hgu95aprobe", "id": "hgu95a" }, "children": [ ] }, { "data": "hgu95av2 (4)", "attr": { "packageList": "hgu95av2,hgu95av2.db,hgu95av2cdf,hgu95av2probe", "id": "hgu95av2" }, "children": [ ] }, { "data": "hgu95b (3)", "attr": { "packageList": "hgu95b.db,hgu95bcdf,hgu95bprobe", "id": "hgu95b" }, "children": [ ] }, { "data": "hgu95c (3)", "attr": { "packageList": "hgu95c.db,hgu95ccdf,hgu95cprobe", "id": "hgu95c" }, "children": [ ] }, { "data": "hgu95d (3)", "attr": { "packageList": "hgu95d.db,hgu95dcdf,hgu95dprobe", "id": "hgu95d" }, "children": [ ] }, { "data": "hgu95e (3)", "attr": { "packageList": "hgu95e.db,hgu95ecdf,hgu95eprobe", "id": "hgu95e" }, "children": [ ] }, { "data": "hguatlas13k (1)", "attr": { "packageList": "hguatlas13k.db", "id": "hguatlas13k" }, "children": [ ] }, { "data": "hgug4100a (1)", "attr": { "packageList": "hgug4100a.db", "id": "hgug4100a" }, "children": [ ] }, { "data": "hgug4101a (1)", "attr": { "packageList": "hgug4101a.db", "id": "hgug4101a" }, "children": [ ] }, { "data": "hgug4110b (1)", "attr": { "packageList": "hgug4110b.db", "id": "hgug4110b" }, "children": [ ] }, { "data": "hgug4111a (1)", "attr": { "packageList": "hgug4111a.db", "id": "hgug4111a" }, "children": [ ] }, { "data": "hgug4112a (1)", "attr": { "packageList": "hgug4112a.db", "id": "hgug4112a" }, "children": [ ] }, { "data": "hguqiagenv3 (1)", "attr": { "packageList": "hguqiagenv3.db", "id": "hguqiagenv3" }, "children": [ ] }, { "data": "hi16cod (1)", "attr": { "packageList": "hi16cod.db", "id": "hi16cod" }, "children": [ ] }, { "data": "hs25kresogen (1)", "attr": { "packageList": "hs25kresogen.db", "id": "hs25kresogen" }, "children": [ ] }, { "data": "hu35ksuba (3)", "attr": { "packageList": "hu35ksuba.db,hu35ksubacdf,hu35ksubaprobe", "id": "hu35ksuba" }, "children": [ ] }, { "data": "hu35ksubb (3)", "attr": { "packageList": "hu35ksubb.db,hu35ksubbcdf,hu35ksubbprobe", "id": "hu35ksubb" }, "children": [ ] }, { "data": "hu35ksubc (3)", "attr": { "packageList": "hu35ksubc.db,hu35ksubccdf,hu35ksubcprobe", "id": "hu35ksubc" }, "children": [ ] }, { "data": "hu35ksubd (3)", "attr": { "packageList": "hu35ksubd.db,hu35ksubdcdf,hu35ksubdprobe", "id": "hu35ksubd" }, "children": [ ] }, { "data": "hu6800 (3)", "attr": { "packageList": "hu6800.db,hu6800cdf,hu6800probe", "id": "hu6800" }, "children": [ ] }, { "data": "HuO22 (1)", "attr": { "packageList": "HuO22.db", "id": "HuO22" }, "children": [ ] }, { "data": "hwgcod (1)", "attr": { "packageList": "hwgcod.db", "id": "hwgcod" }, "children": [ ] }, { "data": "illuminaHumanv1 (1)", "attr": { "packageList": "illuminaHumanv1.db", "id": "illuminaHumanv1" }, "children": [ ] }, { "data": "illuminaHumanv2 (1)", "attr": { "packageList": "illuminaHumanv2.db", "id": "illuminaHumanv2" }, "children": [ ] }, { "data": "illuminaMousev1 (1)", "attr": { "packageList": "illuminaMousev1.db", "id": "illuminaMousev1" }, "children": [ ] }, { "data": "illuminaMousev1p1 (1)", "attr": { "packageList": "illuminaMousev1p1.db", "id": "illuminaMousev1p1" }, "children": [ ] }, { "data": "illuminaRatv1 (1)", "attr": { "packageList": "illuminaRatv1.db", "id": "illuminaRatv1" }, "children": [ ] }, { "data": "indac (1)", "attr": { "packageList": "indac.db", "id": "indac" }, "children": [ ] }, { "childnum": 0, "data": "JazaerimetaData", "children": [ ] }, { "childnum": 0, "data": "lumiHumanV1", "children": [ ] }, { "childnum": 0, "data": "lumiHumanV2", "children": [ ] }, { "childnum": 0, "data": "lumiMouseV1", "children": [ ] }, { "childnum": 0, "data": "lumiRatV1", "children": [ ] }, { "data": "m10kcod (1)", "attr": { "packageList": "m10kcod.db", "id": "m10kcod" }, "children": [ ] }, { "data": "m20kcod (1)", "attr": { "packageList": "m20kcod.db", "id": "m20kcod" }, "children": [ ] }, { "data": "mgu74a (3)", "attr": { "packageList": "mgu74a.db,mgu74acdf,mgu74aprobe", "id": "mgu74a" }, "children": [ ] }, { "data": "mgu74av2 (3)", "attr": { "packageList": "mgu74av2.db,mgu74av2cdf,mgu74av2probe", "id": "mgu74av2" }, "children": [ ] }, { "data": "mgu74b (3)", "attr": { "packageList": "mgu74b.db,mgu74bcdf,mgu74bprobe", "id": "mgu74b" }, "children": [ ] }, { "data": "mgu74bv2 (3)", "attr": { "packageList": "mgu74bv2.db,mgu74bv2cdf,mgu74bv2probe", "id": "mgu74bv2" }, "children": [ ] }, { "data": "mgu74c (3)", "attr": { "packageList": "mgu74c.db,mgu74ccdf,mgu74cprobe", "id": "mgu74c" }, "children": [ ] }, { "data": "mgu74cv2 (3)", "attr": { "packageList": "mgu74cv2.db,mgu74cv2cdf,mgu74cv2probe", "id": "mgu74cv2" }, "children": [ ] }, { "data": "mguatlas5k (1)", "attr": { "packageList": "mguatlas5k.db", "id": "mguatlas5k" }, "children": [ ] }, { "data": "mgug4121a (1)", "attr": { "packageList": "mgug4121a.db", "id": "mgug4121a" }, "children": [ ] }, { "data": "mgug4122a (1)", "attr": { "packageList": "mgug4122a.db", "id": "mgug4122a" }, "children": [ ] }, { "data": "mi16cod (1)", "attr": { "packageList": "mi16cod.db", "id": "mi16cod" }, "children": [ ] }, { "data": "mm24kresogen (1)", "attr": { "packageList": "mm24kresogen.db", "id": "mm24kresogen" }, "children": [ ] }, { "data": "moe430a (3)", "attr": { "packageList": "moe430a.db,moe430acdf,moe430aprobe", "id": "moe430a" }, "children": [ ] }, { "data": "moe430b (3)", "attr": { "packageList": "moe430b.db,moe430bcdf,moe430bprobe", "id": "moe430b" }, "children": [ ] }, { "data": "mouse4302 (4)", "attr": { "packageList": "mouse4302.db,mouse4302cdf,mouse4302frmavecs,mouse4302probe", "id": "mouse4302" }, "children": [ ] }, { "data": "mouse430a2 (4)", "attr": { "packageList": "mouse430a2.db,mouse430a2cdf,mouse430a2frmavecs,mouse430a2probe", "id": "mouse430a2" }, "children": [ ] }, { "data": "mpedbarray (1)", "attr": { "packageList": "mpedbarray.db", "id": "mpedbarray" }, "children": [ ] }, { "data": "mu11ksuba (3)", "attr": { "packageList": "mu11ksuba.db,mu11ksubacdf,mu11ksubaprobe", "id": "mu11ksuba" }, "children": [ ] }, { "data": "mu11ksubb (3)", "attr": { "packageList": "mu11ksubb.db,mu11ksubbcdf,mu11ksubbprobe", "id": "mu11ksubb" }, "children": [ ] }, { "data": "Mu15v1 (1)", "attr": { "packageList": "Mu15v1.db", "id": "Mu15v1" }, "children": [ ] }, { "data": "mu19ksuba (2)", "attr": { "packageList": "mu19ksuba.db,mu19ksubacdf", "id": "mu19ksuba" }, "children": [ ] }, { "data": "mu19ksubb (2)", "attr": { "packageList": "mu19ksubb.db,mu19ksubbcdf", "id": "mu19ksubb" }, "children": [ ] }, { "data": "mu19ksubc (2)", "attr": { "packageList": "mu19ksubc.db,mu19ksubccdf", "id": "mu19ksubc" }, "children": [ ] }, { "data": "Mu22v3 (1)", "attr": { "packageList": "Mu22v3.db", "id": "Mu22v3" }, "children": [ ] }, { "data": "mwgcod (1)", "attr": { "packageList": "mwgcod.db", "id": "mwgcod" }, "children": [ ] }, { "data": "Norway981 (1)", "attr": { "packageList": "Norway981.db", "id": "Norway981" }, "children": [ ] }, { "data": "OperonHumanV3 (1)", "attr": { "packageList": "OperonHumanV3.db", "id": "OperonHumanV3" }, "children": [ ] }, { "data": "PartheenMetaData (1)", "attr": { "packageList": "PartheenMetaData.db", "id": "PartheenMetaData" }, "children": [ ] }, { "data": "pedbarrayv10 (1)", "attr": { "packageList": "pedbarrayv10.db", "id": "pedbarrayv10" }, "children": [ ] }, { "data": "pedbarrayv9 (1)", "attr": { "packageList": "pedbarrayv9.db", "id": "pedbarrayv9" }, "children": [ ] }, { "data": "r10kcod (1)", "attr": { "packageList": "r10kcod.db", "id": "r10kcod" }, "children": [ ] }, { "data": "rae230a (3)", "attr": { "packageList": "rae230a.db,rae230acdf,rae230aprobe", "id": "rae230a" }, "children": [ ] }, { "data": "rae230b (3)", "attr": { "packageList": "rae230b.db,rae230bcdf,rae230bprobe", "id": "rae230b" }, "children": [ ] }, { "data": "rat2302 (4)", "attr": { "packageList": "rat2302.db,rat2302cdf,rat2302frmavecs,rat2302probe", "id": "rat2302" }, "children": [ ] }, { "data": "rgu34a (3)", "attr": { "packageList": "rgu34a.db,rgu34acdf,rgu34aprobe", "id": "rgu34a" }, "children": [ ] }, { "data": "rgu34b (3)", "attr": { "packageList": "rgu34b.db,rgu34bcdf,rgu34bprobe", "id": "rgu34b" }, "children": [ ] }, { "data": "rgu34c (3)", "attr": { "packageList": "rgu34c.db,rgu34ccdf,rgu34cprobe", "id": "rgu34c" }, "children": [ ] }, { "data": "rgug4130a (1)", "attr": { "packageList": "rgug4130a.db", "id": "rgug4130a" }, "children": [ ] }, { "data": "ri16cod (1)", "attr": { "packageList": "ri16cod.db", "id": "ri16cod" }, "children": [ ] }, { "data": "rnu34 (3)", "attr": { "packageList": "rnu34.db,rnu34cdf,rnu34probe", "id": "rnu34" }, "children": [ ] }, { "data": "Roberts2005Annotation (1)", "attr": { "packageList": "Roberts2005Annotation.db", "id": "Roberts2005Annotation" }, "children": [ ] }, { "data": "rtu34 (3)", "attr": { "packageList": "rtu34.db,rtu34cdf,rtu34probe", "id": "rtu34" }, "children": [ ] }, { "data": "rwgcod (1)", "attr": { "packageList": "rwgcod.db", "id": "rwgcod" }, "children": [ ] }, { "data": "SHDZ (1)", "attr": { "packageList": "SHDZ.db", "id": "SHDZ" }, "children": [ ] }, { "data": "u133x3p (3)", "attr": { "packageList": "u133x3p.db,u133x3pcdf,u133x3pprobe", "id": "u133x3p" }, "children": [ ] }, { "data": "xenopuslaevis (2)", "attr": { "packageList": "xenopuslaeviscdf,xenopuslaevisprobe", "id": "xenopuslaevis" }, "children": [ ] }, { "data": "yeast2 (3)", "attr": { "packageList": "yeast2.db,yeast2cdf,yeast2probe", "id": "yeast2" }, "children": [ ] }, { "data": "ygs98 (4)", "attr": { "packageList": "ygs98.db,ygs98cdf,ygs98frmavecs,ygs98probe", "id": "ygs98" }, "children": [ ] }, { "data": "zebrafish (3)", "attr": { "packageList": "zebrafish.db,zebrafishcdf,zebrafishprobe", "id": "zebrafish" }, "children": [ ] } ] }, { "data": "CustomArray (2)", "attr": { "packageList": "hgubeta7.db,hguDKFZ31.db", "id": "CustomArray" }, "children": [ ] }, { "childnum": 0, "data": "CustomCDF", "children": [ { "childnum": 0, "data": "GACustomCDF", "children": [ ] }, { "childnum": 0, "data": "MBNICustomCDF", "children": [ ] } ] }, { "data": "CustomDBSchema (6)", "attr": { "packageList": "ChemmineDrugs,ENCODExplorerData,hpAnnot,metaboliteIDmapping,RmiR.Hs.miRNA,RmiR.hsa", "id": "CustomDBSchema" }, "children": [ { "childnum": 0, "data": "GeneCardsCustomSchema", "children": [ ] } ] }, { "data": "FunctionalAnnotation (31)", "attr": { "packageList": "DO.db,geneplast.data.string.v91,GO.db,hpAnnot,humanCHRLOC,JASPAR2018,JASPAR2020,KEGG.db,LowMACAAnnotation,LRBase.Ath.eg.db,LRBase.Bta.eg.db,LRBase.Cel.eg.db,LRBase.Dme.eg.db,LRBase.Dre.eg.db,LRBase.Gga.eg.db,LRBase.Hsa.eg.db,LRBase.Mmu.eg.db,LRBase.Pab.eg.db,LRBase.Rno.eg.db,LRBase.Ssc.eg.db,LRBase.Xtr.eg.db,MeSH.AOR.db,MeSH.db,MeSH.PCR.db,metaboliteIDmapping,mirbase.db,mouseCHRLOC,ratCHRLOC,reactome.db,targetscan.Hs.eg.db,targetscan.Mm.eg.db", "id": "FunctionalAnnotation" }, "children": [ ] }, { "data": "Organism (634)", "attr": { "packageList": "EpiTxDb.Hs.hg38,EpiTxDb.Mm.mm10,EpiTxDb.Sc.sacCer3,GenomeInfoDbData", "id": "Organism" }, "children": [ { "data": "Anopheles_gambiae (4)", "attr": { "packageList": "anopheles.db0,org.Ag.eg.db,plasmodiumanophelescdf,plasmodiumanophelesprobe", "id": "Anopheles_gambiae" }, "children": [ ] }, { "data": "Apis_mellifera (4)", "attr": { "packageList": "BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.NCBI.AmelHAv3.1,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked", "id": "Apis_mellifera" }, "children": [ ] }, { "childnum": 0, "data": "Arabidopsis_lyrata", "children": [ ] }, { "data": "Arabidopsis_thaliana (14)", "attr": { "packageList": "ag.db,agcdf,agprobe,arabidopsis.db0,ath1121501.db,ath1121501cdf,ath1121501probe,BSgenome.Athaliana.TAIR.04232008,BSgenome.Athaliana.TAIR.TAIR9,hom.At.inp.db,org.At.tair.db,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Athaliana.BioMart.plantsmart25,TxDb.Athaliana.BioMart.plantsmart28", "id": "Arabidopsis_thaliana" }, "children": [ ] }, { "data": "Asparagus_officinalis (1)", "attr": { "packageList": "BSgenome.Aofficinalis.NCBI.V1", "id": "Asparagus_officinalis" }, "children": [ ] }, { "data": "Bacillus_subtilis (2)", "attr": { "packageList": "bsubtiliscdf,bsubtilisprobe", "id": "Bacillus_subtilis" }, "children": [ ] }, { "data": "Bos_taurus (15)", "attr": { "packageList": "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,org.Bt.eg.db,TxDb.Btaurus.UCSC.bosTau8.refGene,TxDb.Btaurus.UCSC.bosTau9.refGene", "id": "Bos_taurus" }, "children": [ ] }, { "data": "Caenorhabditis_elegans (13)", "attr": { "packageList": "BSgenome.Celegans.UCSC.ce10,BSgenome.Celegans.UCSC.ce11,BSgenome.Celegans.UCSC.ce2,BSgenome.Celegans.UCSC.ce6,celegans.db,celeganscdf,celegansprobe,hom.Ce.inp.db,org.Ce.eg.db,TxDb.Celegans.UCSC.ce11.ensGene,TxDb.Celegans.UCSC.ce11.refGene,TxDb.Celegans.UCSC.ce6.ensGene,worm.db0", "id": "Caenorhabditis_elegans" }, "children": [ ] }, { "data": "Callithrix_jacchus (1)", "attr": { "packageList": "BSgenome.Cjacchus.UCSC.calJac3", "id": "Callithrix_jacchus" }, "children": [ ] }, { "data": "Canis_familiaris (13)", "attr": { "packageList": "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", "id": "Canis_familiaris" }, "children": [ ] }, { "data": "Chlamydomonas_reinhardtii (1)", "attr": { "packageList": "BSgenome.Creinhardtii.JGI.v5.6", "id": "Chlamydomonas_reinhardtii" }, "children": [ ] }, { "data": "Cicer_arietinum (1)", "attr": { "packageList": "BSgenome.Carietinum.NCBI.v1", "id": "Cicer_arietinum" }, "children": [ ] }, { "childnum": 0, "data": "Ciona_intestinalis", "children": [ ] }, { "data": "Danio_rerio (16)", "attr": { "packageList": "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,hom.Dr.inp.db,org.Dr.eg.db,TxDb.Drerio.UCSC.danRer10.refGene,TxDb.Drerio.UCSC.danRer11.refGene,zebrafish.db,zebrafish.db0,zebrafishcdf,zebrafishprobe", "id": "Danio_rerio" }, "children": [ ] }, { "data": "Drosophila_melanogaster (17)", "attr": { "packageList": "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,hom.Dm.inp.db,indac.db,org.Dm.eg.db,TxDb.Dmelanogaster.UCSC.dm3.ensGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene", "id": "Drosophila_melanogaster" }, "children": [ ] }, { "data": "Drosophila_virilis (1)", "attr": { "packageList": "BSgenome.Dvirilis.Ensembl.dvircaf1", "id": "Drosophila_virilis" }, "children": [ ] }, { "childnum": 0, "data": "Eremothecium_gossypii", "children": [ ] }, { "data": "Escherichia_coli (12)", "attr": { "packageList": "BSgenome.Ecoli.NCBI.20080805,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliK12.db0,ecoliprobe,ecoliSakai.db0,org.EcK12.eg.db,org.EcSakai.eg.db", "id": "Escherichia_coli" }, "children": [ ] }, { "data": "Gallus_gallus (14)", "attr": { "packageList": "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", "id": "Gallus_gallus" }, "children": [ ] }, { "data": "Gasterosteus_aculeatus (2)", "attr": { "packageList": "BSgenome.Gaculeatus.UCSC.gasAcu1,BSgenome.Gaculeatus.UCSC.gasAcu1.masked", "id": "Gasterosteus_aculeatus" }, "children": [ ] }, { "childnum": 0, "data": "Glycine_max", "children": [ ] }, { "data": "Homo_sapiens (236)", "attr": { "packageList": "BSgenome.Hsapiens.1000genomes.hs37d5,BSgenome.Hsapiens.NCBI.GRCh38,BSgenome.Hsapiens.UCSC.hg17,BSgenome.Hsapiens.UCSC.hg17.masked,BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg18.masked,BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19.masked,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38.masked,clariomdhumanprobeset.db,clariomdhumantranscriptcluster.db,clariomshumanhttranscriptcluster.db,clariomshumantranscriptcluster.db,cyp450cdf,ENCODExplorerData,EnsDb.Hsapiens.v75,EnsDb.Hsapiens.v79,EnsDb.Hsapiens.v86,EpiTxDb.Hs.hg38,FDb.FANTOM4.promoters.hg19,FDb.InfiniumMethylation.hg18,FDb.InfiniumMethylation.hg19,FDb.UCSC.snp135common.hg19,FDb.UCSC.snp137common.hg19,FDb.UCSC.tRNAs,fitCons.UCSC.hg19,GenomicState,GGHumanMethCancerPanelv1.db,gp53cdf,h10kcod.db,h20kcod.db,hcg110.db,hcg110cdf,hcg110probe,hgfocus.db,hgfocuscdf,hgfocusprobe,hgu133a.db,hgu133a2.db,hgu133a2cdf,hgu133a2frmavecs,hgu133a2probe,hgu133acdf,hgu133afrmavecs,hgu133aprobe,hgu133atagcdf,hgu133atagprobe,hgu133b.db,hgu133bcdf,hgu133bprobe,hgu133plus2.db,hgu133plus2cdf,hgu133plus2frmavecs,hgu133plus2probe,hgu219.db,hgu219cdf,hgu219probe,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,hgubeta7.db,hguDKFZ31.db,hgug4100a.db,hgug4101a.db,hgug4110b.db,hgug4111a.db,hgug4112a.db,hgug4845a.db,hguqiagenv3.db,hi16cod.db,hivprtplus2cdf,hom.Hs.inp.db,Homo.sapiens,hs25kresogen.db,Hs6UG171.db,HsAgilentDesign026652.db,Hspec,hspeccdf,hta20probeset.db,hta20transcriptcluster.db,hthgu133a.db,hthgu133acdf,hthgu133afrmavecs,hthgu133aprobe,hthgu133b.db,hthgu133bcdf,hthgu133bprobe,hthgu133pluspmcdf,hthgu133pluspmprobe,hu35ksuba.db,hu35ksubacdf,hu35ksubaprobe,hu35ksubb.db,hu35ksubbcdf,hu35ksubbprobe,hu35ksubc.db,hu35ksubccdf,hu35ksubcprobe,hu35ksubd.db,hu35ksubdcdf,hu35ksubdprobe,hu6800.db,hu6800cdf,hu6800probe,hu6800subacdf,hu6800subbcdf,hu6800subccdf,hu6800subdcdf,huex.1.0.st.v2frmavecs,huex10stprobeset.db,huex10sttranscriptcluster.db,HuExExonProbesetLocation,HuExExonProbesetLocationHg18,HuExExonProbesetLocationHg19,hugene.1.0.st.v1frmavecs,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene10stv1cdf,hugene10stv1probe,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,human.db0,humanCHRLOC,HuO22.db,hwgcod.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kanno.ilmn12.hg19,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylation450kprobe,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,IlluminaHumanMethylationEPICanno.ilm10b3.hg19,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,IlluminaHumanMethylationEPICmanifest,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,JazaeriMetaData.db,LAPOINTE.db,lumiHumanAll.db,MafDb.1Kgenomes.phase1.GRCh38,MafDb.1Kgenomes.phase1.hs37d5,MafDb.1Kgenomes.phase3.GRCh38,MafDb.1Kgenomes.phase3.hs37d5,MafDb.ExAC.r1.0.GRCh38,MafDb.ExAC.r1.0.hs37d5,MafDb.ExAC.r1.0.nonTCGA.GRCh38,MafDb.ExAC.r1.0.nonTCGA.hs37d5,MafDb.gnomAD.r2.1.GRCh38,MafDb.gnomAD.r2.1.hs37d5,MafDb.gnomAD.r3.0.GRCh38,MafDb.gnomADex.r2.1.GRCh38,MafDb.gnomADex.r2.1.hs37d5,MafDb.TOPMed.freeze5.hg19,MafDb.TOPMed.freeze5.hg38,MafH5.gnomAD.r3.0.GRCh38,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,mogene.1.0.st.v1frmavecs,Norway981.db,nugohs1a520180.db,nugohs1a520180cdf,nugohs1a520180probe,OperonHumanV3.db,org.Hs.eg.db,PartheenMetaData.db,pedbarrayv10.db,pedbarrayv9.db,phastCons100way.UCSC.hg19,phastCons100way.UCSC.hg38,phastCons30way.UCSC.hg38,phastCons7way.UCSC.hg38,POCRCannotation.db,PolyPhen.Hsapiens.dbSNP131,primeviewcdf,primeviewprobe,RmiR.Hs.miRNA,RmiR.hsa,Roberts2005Annotation.db,SHDZ.db,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP142.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP151.GRCh38,test1cdf,test2cdf,test3cdf,test3probe,TxDb.Hsapiens.BioMart.igis,TxDb.Hsapiens.UCSC.hg18.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,TxDb.Hsapiens.UCSC.hg38.knownGene,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38", "id": "Homo_sapiens" }, "children": [ ] }, { "data": "Hordeum_vulgare (2)", "attr": { "packageList": "barley1cdf,barley1probe", "id": "Hordeum_vulgare" }, "children": [ ] }, { "childnum": 0, "data": "Kluyveromyces_lactis", "children": [ ] }, { "data": "Macaca_fascicularis (1)", "attr": { "packageList": "BSgenome.Mfascicularis.NCBI.5.0", "id": "Macaca_fascicularis" }, "children": [ ] }, { "data": "Macaca_mulatta (12)", "attr": { "packageList": "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", "id": "Macaca_mulatta" }, "children": [ ] }, { "childnum": 0, "data": "Magnaporthe_grisea", "children": [ ] }, { "childnum": 0, "data": "Medicago_truncatula", "children": [ ] }, { "data": "Monodelphis_domestica (1)", "attr": { "packageList": "BSgenome.Mdomestica.UCSC.monDom5", "id": "Monodelphis_domestica" }, "children": [ ] }, { "data": "Mus_musculus (110)", "attr": { "packageList": "BSgenome.Mmusculus.UCSC.mm10,BSgenome.Mmusculus.UCSC.mm10.masked,BSgenome.Mmusculus.UCSC.mm8,BSgenome.Mmusculus.UCSC.mm8.masked,BSgenome.Mmusculus.UCSC.mm9,BSgenome.Mmusculus.UCSC.mm9.masked,clariomsmousehttranscriptcluster.db,clariomsmousetranscriptcluster.db,ENCODExplorerData,EnsDb.Mmusculus.v75,EnsDb.Mmusculus.v79,EpiTxDb.Mm.mm10,hom.Mm.inp.db,htmg430acdf,htmg430aprobe,htmg430bcdf,htmg430bprobe,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,TxDb.Mmusculus.UCSC.mm10.ensGene,TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm39.refGene,TxDb.Mmusculus.UCSC.mm9.knownGene", "id": "Mus_musculus" }, "children": [ ] }, { "childnum": 0, "data": "Neurospora_crassa", "children": [ ] }, { "childnum": 0, "data": "Oncorhynchus_mykiss", "children": [ ] }, { "data": "Oryza_sativa (1)", "attr": { "packageList": "BSgenome.Osativa.MSU.MSU7", "id": "Oryza_sativa" }, "children": [ ] }, { "data": "Pan_paniscus (2)", "attr": { "packageList": "BSgenome.Ppaniscus.UCSC.panPan1,BSgenome.Ppaniscus.UCSC.panPan2", "id": "Pan_paniscus" }, "children": [ ] }, { "data": "Pan_troglodytes (11)", "attr": { "packageList": "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", "id": "Pan_troglodytes" }, "children": [ ] }, { "data": "Plasmodium_falciparum (4)", "attr": { "packageList": "malaria.db0,org.Pf.plasmo.db,plasmodiumanophelescdf,plasmodiumanophelesprobe", "id": "Plasmodium_falciparum" }, "children": [ ] }, { "data": "Pseudomonas_aeruginosa (2)", "attr": { "packageList": "paeg1acdf,paeg1aprobe", "id": "Pseudomonas_aeruginosa" }, "children": [ ] }, { "data": "Rattus_norvegicus (75)", "attr": { "packageList": "adme16cod.db,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Rnorvegicus.UCSC.rn6,clariomsrathttranscriptcluster.db,clariomsrattranscriptcluster.db,EnsDb.Rnorvegicus.v75,EnsDb.Rnorvegicus.v79,hom.Rn.inp.db,htrat230pmcdf,htrat230pmprobe,htratfocuscdf,htratfocusprobe,illuminaRatv1.db,lumiRatAll.db,org.Rn.eg.db,r10kcod.db,rae230a.db,rae230acdf,rae230aprobe,rae230b.db,rae230bcdf,rae230bprobe,raex10stprobeset.db,raex10sttranscriptcluster.db,ragene10stprobeset.db,ragene10sttranscriptcluster.db,ragene10stv1cdf,ragene10stv1probe,ragene11stprobeset.db,ragene11sttranscriptcluster.db,ragene20stprobeset.db,ragene20sttranscriptcluster.db,ragene21stprobeset.db,ragene21sttranscriptcluster.db,rat.db0,rat2302.db,rat2302cdf,rat2302frmavecs,rat2302probe,ratCHRLOC,rattoxfxcdf,rattoxfxprobe,Rattus.norvegicus,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rguatlas4k.db,rgug4105a.db,rgug4130a.db,rgug4131a.db,ri16cod.db,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,rta10probeset.db,rta10transcriptcluster.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene,TxDb.Rnorvegicus.UCSC.rn6.ncbiRefSeq,TxDb.Rnorvegicus.UCSC.rn6.refGene", "id": "Rattus_norvegicus" }, "children": [ ] }, { "data": "Saccharomyces_cerevisiae (19)", "attr": { "packageList": "BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,EpiTxDb.Sc.sacCer3,hom.Sc.inp.db,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", "id": "Saccharomyces_cerevisiae" }, "children": [ ] }, { "data": "Saccharum_officinarum (2)", "attr": { "packageList": "sugarcanecdf,sugarcaneprobe", "id": "Saccharum_officinarum" }, "children": [ ] }, { "childnum": 0, "data": "Schizosaccharomyces_pombe", "children": [ ] }, { "data": "Staphylococcus_aureus (2)", "attr": { "packageList": "saureuscdf,saureusprobe", "id": "Staphylococcus_aureus" }, "children": [ ] }, { "data": "Sus_scrofa (10)", "attr": { "packageList": "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", "id": "Sus_scrofa" }, "children": [ ] }, { "data": "Taeniopygia_guttata (3)", "attr": { "packageList": "BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,BSgenome.Tguttata.UCSC.taeGut2", "id": "Taeniopygia_guttata" }, "children": [ ] }, { "data": "Toxoplasma_gondii (1)", "attr": { "packageList": "BSgenome.Tgondii.ToxoDB.7.0", "id": "Toxoplasma_gondii" }, "children": [ ] }, { "childnum": 0, "data": "Triticum_aestivum", "children": [ ] }, { "data": "Vitis_vinifera (5)", "attr": { "packageList": "BSgenome.Vvinifera.URGI.IGGP12Xv0,BSgenome.Vvinifera.URGI.IGGP12Xv2,BSgenome.Vvinifera.URGI.IGGP8X,vitisviniferacdf,vitisviniferaprobe", "id": "Vitis_vinifera" }, "children": [ ] }, { "data": "Xenopus_laevis (3)", "attr": { "packageList": "org.Xl.eg.db,xenopus.db0,xlaevis.db", "id": "Xenopus_laevis" }, "children": [ ] }, { "data": "Xenopus_tropicalis (1)", "attr": { "packageList": "xtropicalisprobe", "id": "Xenopus_tropicalis" }, "children": [ ] }, { "data": "Zea_mays (2)", "attr": { "packageList": "maizecdf,maizeprobe", "id": "Zea_mays" }, "children": [ ] } ] }, { "data": "PackageType (681)", "attr": { "packageList": "hpAnnot,rat2302frmavecs", "id": "PackageType" }, "children": [ { "data": "AnnotationHub (11)", "attr": { "packageList": "ENCODExplorerData,EpiTxDb.Hs.hg38,EpiTxDb.Mm.mm10,EpiTxDb.Sc.sacCer3,EuPathDB,geneplast.data,GenomicState,metaboliteIDmapping,org.Mxanthus.db,PANTHER.db,phastCons30way.UCSC.hg38", "id": "AnnotationHub" }, "children": [ ] }, { "data": "BSgenome (100)", "attr": { "packageList": "BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.NCBI.AmelHAv3.1,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,BSgenome.Aofficinalis.NCBI.V1,BSgenome.Athaliana.TAIR.04232008,BSgenome.Athaliana.TAIR.TAIR9,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.Carietinum.NCBI.v1,BSgenome.Celegans.UCSC.ce10,BSgenome.Celegans.UCSC.ce11,BSgenome.Celegans.UCSC.ce2,BSgenome.Celegans.UCSC.ce6,BSgenome.Cfamiliaris.UCSC.canFam2,BSgenome.Cfamiliaris.UCSC.canFam2.masked,BSgenome.Cfamiliaris.UCSC.canFam3,BSgenome.Cfamiliaris.UCSC.canFam3.masked,BSgenome.Cjacchus.UCSC.calJac3,BSgenome.Creinhardtii.JGI.v5.6,BSgenome.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,BSgenome.Dmelanogaster.UCSC.dm6,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,BSgenome.Dvirilis.Ensembl.dvircaf1,BSgenome.Ecoli.NCBI.20080805,BSgenome.Gaculeatus.UCSC.gasAcu1,BSgenome.Gaculeatus.UCSC.gasAcu1.masked,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,BSgenome.Hsapiens.1000genomes.hs37d5,BSgenome.Hsapiens.NCBI.GRCh38,BSgenome.Hsapiens.UCSC.hg17,BSgenome.Hsapiens.UCSC.hg17.masked,BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg18.masked,BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19.masked,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38.masked,BSgenome.Mdomestica.UCSC.monDom5,BSgenome.Mfascicularis.NCBI.5.0,BSgenome.Mfuro.UCSC.musFur1,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,BSgenome.Mmusculus.UCSC.mm10,BSgenome.Mmusculus.UCSC.mm10.masked,BSgenome.Mmusculus.UCSC.mm8,BSgenome.Mmusculus.UCSC.mm8.masked,BSgenome.Mmusculus.UCSC.mm9,BSgenome.Mmusculus.UCSC.mm9.masked,BSgenome.Osativa.MSU.MSU7,BSgenome.Ppaniscus.UCSC.panPan1,BSgenome.Ppaniscus.UCSC.panPan2,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,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Rnorvegicus.UCSC.rn6,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr11,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,BSgenome.Tguttata.UCSC.taeGut2,BSgenome.Vvinifera.URGI.IGGP12Xv0,BSgenome.Vvinifera.URGI.IGGP12Xv2,BSgenome.Vvinifera.URGI.IGGP8X", "id": "BSgenome" }, "children": [ ] }, { "data": "cdf (118)", "attr": { "packageList": "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", "id": "cdf" }, "children": [ ] }, { "data": "ChipDb (167)", "attr": { "packageList": "adme16cod.db,ag.db,ath1121501.db,bovine.db,canine.db,canine2.db,celegans.db,chicken.db,clariomdhumanprobeset.db,clariomdhumantranscriptcluster.db,clariomshumanhttranscriptcluster.db,clariomshumantranscriptcluster.db,clariomsmousehttranscriptcluster.db,clariomsmousetranscriptcluster.db,clariomsrathttranscriptcluster.db,clariomsrattranscriptcluster.db,drosgenome1.db,drosophila2.db,ecoli2.db,h10kcod.db,h20kcod.db,hcg110.db,hgfocus.db,hgu133a.db,hgu133a2.db,hgu133b.db,hgu133plus2.db,hgu219.db,hgu95a.db,hgu95av2.db,hgu95b.db,hgu95c.db,hgu95d.db,hgu95e.db,hguatlas13k.db,hgubeta7.db,hguDKFZ31.db,hgug4100a.db,hgug4101a.db,hgug4110b.db,hgug4111a.db,hgug4112a.db,hguqiagenv3.db,hi16cod.db,Hs6UG171.db,HsAgilentDesign026652.db,hta20probeset.db,hta20transcriptcluster.db,hthgu133a.db,hthgu133b.db,hu35ksuba.db,hu35ksubb.db,hu35ksubc.db,hu35ksubd.db,hu6800.db,huex10stprobeset.db,huex10sttranscriptcluster.db,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,HuO22.db,hwgcod.db,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,illuminaMousev1.db,illuminaMousev1p1.db,illuminaMousev2.db,illuminaRatv1.db,indac.db,JazaeriMetaData.db,LAPOINTE.db,lumiHumanAll.db,lumiMouseAll.db,lumiRatAll.db,m10kcod.db,m20kcod.db,mgu74a.db,mgu74av2.db,mgu74b.db,mgu74bv2.db,mgu74c.db,mgu74cv2.db,mguatlas5k.db,mgug4104a.db,mgug4120a.db,mgug4121a.db,mgug4122a.db,mi16cod.db,MmAgilentDesign026655.db,moe430a.db,moe430b.db,moex10stprobeset.db,moex10sttranscriptcluster.db,mogene10stprobeset.db,mogene10sttranscriptcluster.db,mogene11stprobeset.db,mogene11sttranscriptcluster.db,mogene20stprobeset.db,mogene20sttranscriptcluster.db,mogene21stprobeset.db,mogene21sttranscriptcluster.db,mouse4302.db,mouse430a2.db,mpedbarray.db,mta10probeset.db,mta10transcriptcluster.db,mu11ksuba.db,mu11ksubb.db,Mu15v1.db,mu19ksuba.db,mu19ksubb.db,mu19ksubc.db,Mu22v3.db,mwgcod.db,Norway981.db,nugohs1a520180.db,nugomm1a520177.db,OperonHumanV3.db,PartheenMetaData.db,pedbarrayv10.db,pedbarrayv9.db,POCRCannotation.db,porcine.db,r10kcod.db,rae230a.db,rae230b.db,raex10stprobeset.db,raex10sttranscriptcluster.db,ragene10stprobeset.db,ragene10sttranscriptcluster.db,ragene11stprobeset.db,ragene11sttranscriptcluster.db,ragene20stprobeset.db,ragene20sttranscriptcluster.db,ragene21stprobeset.db,ragene21sttranscriptcluster.db,rat2302.db,rgu34a.db,rgu34b.db,rgu34c.db,rguatlas4k.db,rgug4105a.db,rgug4130a.db,rgug4131a.db,ri16cod.db,RnAgilentDesign028282.db,rnu34.db,Roberts2005Annotation.db,rta10probeset.db,rta10transcriptcluster.db,rtu34.db,rwgcod.db,SHDZ.db,u133x3p.db,xlaevis.db,yeast2.db,ygs98.db,zebrafish.db", "id": "ChipDb" }, "children": [ ] }, { "data": "db0 (19)", "attr": { "packageList": "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", "id": "db0" }, "children": [ ] }, { "data": "EuPathDB (1)", "attr": { "packageList": "EuPathDB", "id": "EuPathDB" }, "children": [ ] }, { "data": "FRMA (11)", "attr": { "packageList": "hgu133a2frmavecs,hgu133afrmavecs,hgu133plus2frmavecs,hthgu133afrmavecs,huex.1.0.st.v2frmavecs,hugene.1.0.st.v1frmavecs,mogene.1.0.st.v1frmavecs,mouse4302frmavecs,mouse430a2frmavecs,rat2302frmavecs,ygs98frmavecs", "id": "FRMA" }, "children": [ ] }, { "data": "InparanoidDb (8)", "attr": { "packageList": "hom.At.inp.db,hom.Ce.inp.db,hom.Dm.inp.db,hom.Dr.inp.db,hom.Hs.inp.db,hom.Mm.inp.db,hom.Rn.inp.db,hom.Sc.inp.db", "id": "InparanoidDb" }, "children": [ ] }, { "data": "MeSHDb (78)", "attr": { "packageList": "MeSH.Aca.eg.db,MeSH.Aga.PEST.eg.db,MeSH.Ame.eg.db,MeSH.Aml.eg.db,MeSH.Ana.eg.db,MeSH.Ani.FGSC.eg.db,MeSH.AOR.db,MeSH.Ath.eg.db,MeSH.Bfl.eg.db,MeSH.Bsu.168.eg.db,MeSH.Bta.eg.db,MeSH.Cal.SC5314.eg.db,MeSH.Cbr.eg.db,MeSH.Cel.eg.db,MeSH.Cfa.eg.db,MeSH.Cin.eg.db,MeSH.Cja.eg.db,MeSH.Cpo.eg.db,MeSH.Cre.eg.db,MeSH.Dan.eg.db,MeSH.db,MeSH.Dda.3937.eg.db,MeSH.Ddi.AX4.eg.db,MeSH.Der.eg.db,MeSH.Dgr.eg.db,MeSH.Dme.eg.db,MeSH.Dmo.eg.db,MeSH.Dpe.eg.db,MeSH.Dre.eg.db,MeSH.Dse.eg.db,MeSH.Dsi.eg.db,MeSH.Dvi.eg.db,MeSH.Dya.eg.db,MeSH.Eca.eg.db,MeSH.Eco.55989.eg.db,MeSH.Eco.ED1a.eg.db,MeSH.Eco.IAI39.eg.db,MeSH.Eco.K12.MG1655.eg.db,MeSH.Eco.O157.H7.Sakai.eg.db,MeSH.Eco.UMN026.eg.db,MeSH.Eqc.eg.db,MeSH.Gga.eg.db,MeSH.Gma.eg.db,MeSH.Hsa.eg.db,MeSH.Laf.eg.db,MeSH.Lma.eg.db,MeSH.Mdo.eg.db,MeSH.Mes.eg.db,MeSH.Mga.eg.db,MeSH.Miy.eg.db,MeSH.Mml.eg.db,MeSH.Mmu.eg.db,MeSH.Mtr.eg.db,MeSH.Nle.eg.db,MeSH.Oan.eg.db,MeSH.Ocu.eg.db,MeSH.Oni.eg.db,MeSH.Osa.eg.db,MeSH.Pab.eg.db,MeSH.Pae.PAO1.eg.db,MeSH.PCR.db,MeSH.Pfa.3D7.eg.db,MeSH.Pto.eg.db,MeSH.Ptr.eg.db,MeSH.Rno.eg.db,MeSH.Sce.S288c.eg.db,MeSH.Sco.A32.eg.db,MeSH.Sil.eg.db,MeSH.Spu.eg.db,MeSH.Ssc.eg.db,MeSH.Syn.eg.db,MeSH.Tbr.9274.eg.db,MeSH.Tgo.ME49.eg.db,MeSH.Tgu.eg.db,MeSH.Vvi.eg.db,MeSH.Xla.eg.db,MeSH.Xtr.eg.db,MeSH.Zma.eg.db", "id": "MeSHDb" }, "children": [ ] }, { "data": "OrganismDb (3)", "attr": { "packageList": "Homo.sapiens,Mus.musculus,Rattus.norvegicus", "id": "OrganismDb" }, "children": [ ] }, { "data": "OrgDb (20)", "attr": { "packageList": "org.Ag.eg.db,org.At.tair.db,org.Bt.eg.db,org.Ce.eg.db,org.Cf.eg.db,org.Dm.eg.db,org.Dr.eg.db,org.EcK12.eg.db,org.EcSakai.eg.db,org.Gg.eg.db,org.Hs.eg.db,org.Mm.eg.db,org.Mmu.eg.db,org.Mxanthus.db,org.Pf.plasmo.db,org.Pt.eg.db,org.Rn.eg.db,org.Sc.sgd.db,org.Ss.eg.db,org.Xl.eg.db", "id": "OrgDb" }, "children": [ ] }, { "childnum": 0, "data": "PolyPhen", "children": [ ] }, { "data": "probe (97)", "attr": { "packageList": "agprobe,ath1121501probe,barley1probe,bovineprobe,bsubtilisprobe,canine2probe,canineprobe,celegansprobe,chickenprobe,citrusprobe,cottonprobe,drosgenome1probe,drosophila2probe,ecoli2probe,ecoliasv2probe,ecoliprobe,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", "id": "probe" }, "children": [ ] }, { "childnum": 0, "data": "SIFT", "children": [ ] }, { "data": "SNPlocs (6)", "attr": { "packageList": "SNPlocs.Hsapiens.dbSNP141.GRCh38,SNPlocs.Hsapiens.dbSNP144.GRCh37,SNPlocs.Hsapiens.dbSNP144.GRCh38,SNPlocs.Hsapiens.dbSNP149.GRCh38,SNPlocs.Hsapiens.dbSNP150.GRCh38,SNPlocs.Hsapiens.dbSNP151.GRCh38", "id": "SNPlocs" }, "children": [ ] }, { "data": "TxDb (42)", "attr": { "packageList": "FDb.UCSC.tRNAs,GenomicState,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Athaliana.BioMart.plantsmart25,TxDb.Athaliana.BioMart.plantsmart28,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.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.hg38.knownGene,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.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.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,TxDb.Sscrofa.UCSC.susScr11.refGene,TxDb.Sscrofa.UCSC.susScr3.refGene", "id": "TxDb" }, "children": [ ] }, { "data": "XtraSNPlocs (3)", "attr": { "packageList": "XtraSNPlocs.Hsapiens.dbSNP141.GRCh38,XtraSNPlocs.Hsapiens.dbSNP144.GRCh37,XtraSNPlocs.Hsapiens.dbSNP144.GRCh38", "id": "XtraSNPlocs" }, "children": [ ] } ] }, { "data": "SequenceAnnotation (1)", "attr": { "packageList": "LymphoSeqDB", "id": "SequenceAnnotation" }, "children": [ { "data": "GenomicSequence (1)", "attr": { "packageList": "LymphoSeqDB", "id": "GenomicSequence" }, "children": [ ] } ] } ] }, { "data": "ExperimentData (398)", "attr": { "packageList": "ABAData,adductData,affycompData,affydata,Affyhgu133A2Expr,Affyhgu133aExpr,Affyhgu133Plus2Expr,AffymetrixDataTestFiles,Affymoe4302Expr,airway,ALL,ALLMLL,alpineData,AmpAffyExample,AneuFinderData,antiProfilesData,aracne.networks,ARRmData,AshkenazimSonChr21,ASICSdata,AssessORFData,bcellViper,beadarrayExampleData,BeadArrayUseCases,benchmarkfdrData2019,beta7,biotmleData,biscuiteerData,bladderbatch,blimaTestingData,BloodCancerMultiOmics2017,bodymapRat,brainImageRdata,breakpointRdata,breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,brgedata,bronchialIL13,bsseqData,cancerdata,CardinalWorkflows,ccdata,CCl4,ccTutorial,celarefData,celldex,CellMapperData,ceu1kg,ceu1kgv,ceuhm3,cgdv17,ChAMPdata,ChIC.data,ChimpHumanBrainData,chipenrich.data,ChIPexoQualExample,chipseqDBData,ChIPXpressData,chromstaRData,CLL,CLLmethylation,CluMSIDdata,clustifyrdatahub,cMap2data,cnvGSAdata,COHCAPanno,colonCA,CONFESSdata,ConnectivityMap,COPDSexualDimorphism.data,CopyhelpeR,CopyNeutralIMA,COSMIC.67,CRCL18,curatedAdipoArray,curatedAdipoChIP,curatedAdipoRNA,curatedBladderData,curatedBreastData,curatedCRCData,curatedMetagenomicData,curatedOvarianData,curatedTCGAData,DAPARdata,davidTiling,depmap,derfinderData,DeSousa2013,diffloopdata,diggitdata,DLBCL,DmelSGI,DMRcatedata,DonaPLLP2013,dorothea,DREAM4,dressCheck,DropletTestFiles,DrugVsDiseasedata,dsQTL,DuoClustering2018,DvDdata,dyebiasexamples,EatonEtAlChIPseq,ecoliLeucine,EGSEAdata,ELMER.data,estrogen,etec16s,faahKO,fabiaData,facsDorit,FANTOM3and4CAGE,ffpeExampleData,fibroEset,FieldEffectCrc,FIs,fission,Fletcher2013a,Fletcher2013b,flowFitExampleData,flowPloidyData,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,flowWorkspaceData,frmaExampleData,FunciSNP.data,furrowSeg,gageData,gaschYHS,gatingMLData,gcspikelite,geneLenDataBase,genomationData,GeuvadisTranscriptExpr,geuvPack,geuvStore2,GGdata,GIGSEAdata,golubEsets,gpaExample,grndata,GSBenchMark,GSE62944,gskb,GSVAdata,GWASdata,h5vcData,hapmap100khind,hapmap100kxba,hapmap500knsp,hapmap500ksty,hapmapsnp5,hapmapsnp6,harbChIP,HarmanData,HarmonizedTCGAData,HCAData,HD2013SGI,HDCytoData,healthyFlowData,HEEBOdata,HelloRangesData,hgu133abarcodevecs,hgu133plus2barcodevecs,hgu133plus2CellScore,hgu2beta7,HiCDataHumanIMR90,HiCDataLymphoblast,HighlyReplicatedRNASeq,Hiiragi2013,HIVcDNAvantWout03,HMP16SData,HMP2Data,hmyriB36,HSMMSingleCell,HumanAffyData,humanStemCell,IHWpaper,Illumina450ProbeVariants.db,IlluminaDataTestFiles,ITALICSData,Iyer517,JASPAR2014,JASPAR2016,JctSeqData,KEGGandMetacoreDzPathwaysGEO,KEGGdzPathwaysGEO,kidpack,KOdata,leeBamViews,leukemiasEset,LiebermanAidenHiC2009,ListerEtAlBSseq,lumiBarnes,LungCancerACvsSCCGEO,LungCancerLines,lungExpression,lydata,M3DExampleData,macrophage,mammaPrintData,mAPKLData,maqcExpression4plex,MAQCsubset,MAQCsubsetAFX,MAQCsubsetILM,mCSEAdata,mcsurvdata,MEDIPSData,MEEBOdata,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,metaMSdata,MethylAidData,MethylSeqData,methyvimData,microRNAome,MIGSAdata,minfiData,minfiDataEPIC,minionSummaryData,miRcompData,miRNATarget,mitoODEdata,MMAPPR2data,MMDiffBamSubset,MOFAdata,mosaicsExample,mouse4302barcodevecs,MouseGastrulationData,msd16s,msdata,MSMB,msPurityData,msqc1,MSstatsBioData,mtbls2,MUGAExampleData,Mulder2012,muscData,mvoutData,NanoporeRNASeq,nanotubes,NCIgraphData,NestLink,Neve2006,NGScopyData,oct4,OMICsPCAdata,OnassisJavaLibs,optimalFlowData,parathyroidSE,pasilla,pasillaBamSubset,PasillaTranscriptExpr,PathNetData,pathprintGEOData,pcaGoPromoter.Hs.hg19,pcaGoPromoter.Mm.mm9,pcaGoPromoter.Rn.rn4,PCHiCdata,pcxnData,pd.atdschip.tiling,pepDat,PepsNMRData,PhyloProfileData,plasFIA,ppiData,prebsdata,PREDAsampledata,ProData,pRolocdata,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally,PtH2O2lipids,pumadata,PWMEnrich.Dmelanogaster.background,PWMEnrich.Hsapiens.background,PWMEnrich.Mmusculus.background,pwrEWAS.data,QDNAseq.hg19,QDNAseq.mm10,qPLEXdata,QUBICdata,rcellminerData,RcisTarget.hg19.motifDBs.cisbpOnly.500bp,ReactomeGSA.data,RegParallel,restfulSEData,RforProteomics,RGMQLlib,rheumaticConditionWOLLBOLD,RITANdata,RMassBankData,RNAinteractMAPK,RNAmodR.Data,RNAseqData.HNRNPC.bam.chr14,RNASeqRData,RnaSeqSampleSizeData,RnBeads.hg19,RnBeads.hg38,RnBeads.mm10,RnBeads.mm9,RnBeads.rn5,RRBSdata,rRDPData,RTCGA.clinical,RTCGA.CNV,RTCGA.methylation,RTCGA.miRNASeq,RTCGA.mRNA,RTCGA.mutations,RTCGA.PANCAN12,RTCGA.rnaseq,RTCGA.RPPA,RUVnormalizeData,sampleClassifierData,SBGNview.data,SCATEData,SCLCBam,scRNAseq,scTHI.data,seq2pathway.data,seqc,seqCNA.annot,serumStimulation,sesameData,seventyGeneData,shinyMethylData,signatureSearchData,simpIntLists,Single.mTEC.Transcriptomes,SingleCellMultiModal,SNAData,SNAGEEdata,SNPhoodData,SomatiCAData,SomaticCancerAlterations,spatialLIBD,SpikeIn,SpikeInSubset,spqnData,stemHypoxia,stjudem,SVM2CRMdata,synapterdata,systemPipeRdata,TabulaMurisData,TargetScoreData,TargetSearchData,tartare,TBX20BamSubset,TCGAbiolinksGUI.data,TCGAcrcmiRNA,TCGAcrcmRNA,TCGAMethylation450k,tcgaWGBSData.hg19,TCGAWorkflowData,TENxBrainData,TENxBUSData,TENxPBMCData,timecoursedata,TimerQuant,tinesath1cdf,tinesath1probe,tissueTreg,TMExplorer,tofsimsData,topdownrdata,tweeDEseqCountData,tximportData,VariantToolsData,vulcandata,waveTilingData,WES.1KG.WUGSC,WGSmapp,XhybCasneuf,yeastCC,yeastExpData,yeastGSData,yeastNagalakshmi,yeastRNASeq,yri1kgv,yriMulti,zebrafishRNASeq", "id": "ExperimentData" }, "children": [ { "data": "AssayDomainData (81)", "attr": { "packageList": "depmap,ELMER.data,TCGAbiolinksGUI.data", "id": "AssayDomainData" }, "children": [ { "data": "CopyNumberVariationData (5)", "attr": { "packageList": "AneuFinderData,cnvGSAdata,depmap,rcellminerData,seqCNA.annot", "id": "CopyNumberVariationData" }, "children": [ ] }, { "data": "CpGIslandData (2)", "attr": { "packageList": "COHCAPanno,RRBSdata", "id": "CpGIslandData" }, "children": [ ] }, { "data": "ExpressionData (56)", "attr": { "packageList": "ABAData,alpineData,benchmarkfdrData2019,bodymapRat,brainImageRdata,ccdata,celldex,CellMapperData,clustifyrdatahub,CONFESSdata,curatedBladderData,curatedBreastData,DropletTestFiles,FieldEffectCrc,Fletcher2013a,GeuvadisTranscriptExpr,HarmanData,HCAData,HDCytoData,hgu133plus2CellScore,HighlyReplicatedRNASeq,HumanAffyData,IHWpaper,KOdata,M3DExampleData,mammaPrintData,mAPKLData,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,miRcompData,MouseGastrulationData,muscData,nanotubes,OMICsPCAdata,PasillaTranscriptExpr,pathprintGEOData,pcxnData,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally,rcellminerData,ReactomeGSA.data,restfulSEData,sampleClassifierData,scRNAseq,signatureSearchData,spatialLIBD,spqnData,TENxBrainData,TENxBUSData,TENxPBMCData,timecoursedata,TMExplorer", "id": "ExpressionData" }, "children": [ ] }, { "data": "SNPData (19)", "attr": { "packageList": "ceu1kg,ceuhm3,cgdv17,DMRcatedata,Fletcher2013b,FunciSNP.data,GeuvadisTranscriptExpr,GGdata,gpaExample,GWASdata,hapmapsnp5,hapmapsnp6,hmyriB36,Illumina450ProbeVariants.db,leeBamViews,pd.atdschip.tiling,pumadata,rcellminerData,VariantToolsData", "id": "SNPData" }, "children": [ ] } ] }, { "data": "DiseaseModel (90)", "attr": { "packageList": "CLLmethylation,depmap,RegParallel", "id": "DiseaseModel" }, "children": [ { "data": "CancerData (87)", "attr": { "packageList": "ALL,ALLMLL,antiProfilesData,aracne.networks,bcellViper,bladderbatch,BloodCancerMultiOmics2017,breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,bsseqData,cancerdata,CLL,CLLmethylation,colonCA,ConnectivityMap,COSMIC.67,CRCL18,curatedBladderData,curatedBreastData,curatedOvarianData,curatedTCGAData,depmap,DeSousa2013,DLBCL,fabiaData,Fletcher2013a,Fletcher2013b,gageData,golubEsets,GSVAdata,h5vcData,hapmap100khind,hapmap100kxba,hapmap500knsp,hapmap500ksty,hapmapsnp5,HarmonizedTCGAData,HD2013SGI,Illumina450ProbeVariants.db,kidpack,KOdata,leukemiasEset,LungCancerACvsSCCGEO,LungCancerLines,lungExpression,mammaPrintData,maqcExpression4plex,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,microRNAome,MIGSAdata,Mulder2012,Neve2006,NGScopyData,PREDAsampledata,ProData,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally,rcellminerData,RnaSeqSampleSizeData,RRBSdata,SBGNview.data,seventyGeneData,shinyMethylData,SomatiCAData,SomaticCancerAlterations,stemHypoxia,stjudem,TCGAcrcmiRNA,TCGAcrcmRNA,TCGAMethylation450k,tcgaWGBSData.hg19,TCGAWorkflowData,TMExplorer,vulcandata,yeastCC", "id": "CancerData" }, "children": [ { "data": "BreastCancerData (18)", "attr": { "packageList": "breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,curatedBreastData,depmap,fabiaData,Fletcher2013a,Fletcher2013b,gageData,mammaPrintData,MIGSAdata,Neve2006,ProData,SBGNview.data,seventyGeneData", "id": "BreastCancerData" }, "children": [ ] }, { "data": "ColonCancerData (7)", "attr": { "packageList": "antiProfilesData,bsseqData,colonCA,depmap,DeSousa2013,FieldEffectCrc,HD2013SGI", "id": "ColonCancerData" }, "children": [ ] }, { "data": "KidneyCancerData (3)", "attr": { "packageList": "depmap,kidpack,PREDAsampledata", "id": "KidneyCancerData" }, "children": [ ] }, { "data": "LeukemiaCancerData (10)", "attr": { "packageList": "ALL,ALLMLL,BloodCancerMultiOmics2017,CLL,CLLmethylation,depmap,golubEsets,GSVAdata,leukemiasEset,stjudem", "id": "LeukemiaCancerData" }, "children": [ ] }, { "data": "LungCancerData (8)", "attr": { "packageList": "AneuFinderData,breastCancerVDX,depmap,LungCancerACvsSCCGEO,LungCancerLines,lungExpression,NGScopyData,SCLCBam", "id": "LungCancerData" }, "children": [ ] }, { "data": "OvarianCancerData (3)", "attr": { "packageList": "curatedBladderData,curatedOvarianData,depmap", "id": "OvarianCancerData" }, "children": [ ] }, { "data": "ProstateCancerData (6)", "attr": { "packageList": "depmap,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally", "id": "ProstateCancerData" }, "children": [ ] } ] }, { "data": "COPDData (1)", "attr": { "packageList": "COPDSexualDimorphism.data", "id": "COPDData" }, "children": [ ] }, { "data": "HIVData (1)", "attr": { "packageList": "HIVcDNAvantWout03", "id": "HIVData" }, "children": [ ] } ] }, { "data": "OrganismData (139)", "attr": { "packageList": "AssessORFData,brainImageRdata,depmap,ELMER.data,PepsNMRData,QDNAseq.hg19,QDNAseq.mm10,QUBICdata,TCGAbiolinksGUI.data", "id": "OrganismData" }, "children": [ { "childnum": 0, "data": "Anopheles_gambiae_Data", "children": [ ] }, { "childnum": 0, "data": "Apis_mellifera_Data", "children": [ ] }, { "childnum": 0, "data": "Arabidopsis_lyrata_Data", "children": [ ] }, { "data": "Arabidopsis_thaliana_Data (6)", "attr": { "packageList": "pd.atdschip.tiling,pRolocdata,simpIntLists,tinesath1cdf,tinesath1probe,waveTilingData", "id": "Arabidopsis_thaliana_Data" }, "children": [ ] }, { "data": "Bacillus_subtilis_Data (1)", "attr": { "packageList": "AssessORFData", "id": "Bacillus_subtilis_Data" }, "children": [ ] }, { "childnum": 0, "data": "Bos_taurus_Data", "children": [ ] }, { "data": "Caenorhabditis_elegans_Data (1)", "attr": { "packageList": "pathprintGEOData", "id": "Caenorhabditis_elegans_Data" }, "children": [ ] }, { "childnum": 0, "data": "Callithrix_jacchus_Data", "children": [ ] }, { "childnum": 0, "data": "Canis_familiaris_Data", "children": [ ] }, { "childnum": 0, "data": "Ciona_intestinalis_Data", "children": [ ] }, { "data": "Danio_rerio_Data (4)", "attr": { "packageList": "MMAPPR2data,pathprintGEOData,TimerQuant,zebrafishRNASeq", "id": "Danio_rerio_Data" }, "children": [ ] }, { "data": "Drosophila_melanogaster_Data (8)", "attr": { "packageList": "DmelSGI,furrowSeg,pasilla,PasillaTranscriptExpr,pathprintGEOData,pRolocdata,PWMEnrich.Dmelanogaster.background,RNAinteractMAPK", "id": "Drosophila_melanogaster_Data" }, "children": [ ] }, { "childnum": 0, "data": "Drosophila_virilis_Data", "children": [ ] }, { "childnum": 0, "data": "Eremothecium_gossypii_Data", "children": [ ] }, { "data": "Escherichia_coli_Data (3)", "attr": { "packageList": "AssessORFData,QUBICdata,TargetSearchData", "id": "Escherichia_coli_Data" }, "children": [ ] }, { "childnum": 0, "data": "Gallus_gallus_Data", "children": [ ] }, { "childnum": 0, "data": "Gasterosteus_aculeatus_Data", "children": [ ] }, { "childnum": 0, "data": "Glycine_max_Data", "children": [ ] }, { "data": "Homo_sapiens_Data (93)", "attr": { "packageList": "ABAData,Affyhgu133A2Expr,Affyhgu133aExpr,Affyhgu133Plus2Expr,AneuFinderData,aracne.networks,ASICSdata,bcellViper,beadarrayExampleData,beta7,biscuiteerData,brainImageRdata,breakpointRdata,breastCancerVDX,brgedata,ChimpHumanBrainData,ChIPXpressData,cMap2data,COHCAPanno,CONFESSdata,CopyNeutralIMA,curatedMetagenomicData,curatedTCGAData,depmap,derfinderData,DMRcatedata,dorothea,DrugVsDiseasedata,EGSEAdata,fibroEset,FieldEffectCrc,FIs,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,frmaExampleData,GeuvadisTranscriptExpr,GIGSEAdata,gpaExample,GSVAdata,HarmanData,HD2013SGI,HDCytoData,hgu133abarcodevecs,hgu133plus2barcodevecs,hgu133plus2CellScore,HiCDataHumanIMR90,HiCDataLymphoblast,HMP16SData,HMP2Data,HumanAffyData,humanStemCell,Illumina450ProbeVariants.db,KOdata,leukemiasEset,ListerEtAlBSseq,MAQCsubsetAFX,MAQCsubsetILM,mCSEAdata,mcsurvdata,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,MethylSeqData,minfiData,minfiDataEPIC,miRcompData,miRNATarget,muscData,pathprintGEOData,pcaGoPromoter.Hs.hg19,PCHiCdata,pcxnData,PepsNMRData,pRolocdata,PWMEnrich.Hsapiens.background,QDNAseq.hg19,RcisTarget.hg19.motifDBs.cisbpOnly.500bp,ReactomeGSA.data,restfulSEData,RNAseqData.HNRNPC.bam.chr14,spatialLIBD,spqnData,stemHypoxia,tcgaWGBSData.hg19,TCGAWorkflowData,tweeDEseqCountData,vulcandata,WES.1KG.WUGSC,WGSmapp", "id": "Homo_sapiens_Data" }, "children": [ ] }, { "childnum": 0, "data": "Hordeum_vulgare_Data", "children": [ ] }, { "childnum": 0, "data": "Kluyveromyces_lactis_Data", "children": [ ] }, { "childnum": 0, "data": "Macaca_mulatta_Data", "children": [ ] }, { "childnum": 0, "data": "Magnaporthe_grisea_Data", "children": [ ] }, { "childnum": 0, "data": "Medicago_truncatul_Data", "children": [ ] }, { "childnum": 0, "data": "Monodelphis_domestica_Data", "children": [ ] }, { "data": "Mus_musculus_Data (21)", "attr": { "packageList": "Affymoe4302Expr,ccTutorial,ChIPXpressData,chromstaRData,DMRcatedata,dorothea,EGSEAdata,HarmanData,M3DExampleData,MethylSeqData,MMDiffBamSubset,mouse4302barcodevecs,MUGAExampleData,pathprintGEOData,pcaGoPromoter.Mm.mm9,PCHiCdata,pRolocdata,PWMEnrich.Mmusculus.background,QDNAseq.mm10,restfulSEData,tissueTreg", "id": "Mus_musculus_Data" }, "children": [ ] }, { "childnum": 0, "data": "Neurospora_crassa_Data", "children": [ ] }, { "childnum": 0, "data": "Oncorhynchus_mykiss_Data", "children": [ ] }, { "childnum": 0, "data": "Oryza_sativa_Data", "children": [ ] }, { "childnum": 0, "data": "Pan_paniscus_Data", "children": [ ] }, { "data": "Pan_troglodytes_Data (1)", "attr": { "packageList": "ChimpHumanBrainData", "id": "Pan_troglodytes_Data" }, "children": [ ] }, { "childnum": 0, "data": "Plasmodium_falciparum_Data", "children": [ ] }, { "data": "Pseudomonas_aeruginosa_Data (1)", "attr": { "packageList": "AssessORFData", "id": "Pseudomonas_aeruginosa_Data" }, "children": [ ] }, { "data": "Rattus_norvegicus_Data (5)", "attr": { "packageList": "CCl4,EGSEAdata,JctSeqData,pathprintGEOData,pcaGoPromoter.Rn.rn4", "id": "Rattus_norvegicus_Data" }, "children": [ ] }, { "data": "Saccharomyces_cerevisiae_Data (13)", "attr": { "packageList": "davidTiling,DREAM4,EatonEtAlChIPseq,fission,gaschYHS,harbChIP,leeBamViews,RNASeqRData,yeastCC,yeastExpData,yeastGSData,yeastNagalakshmi,yeastRNASeq", "id": "Saccharomyces_cerevisiae_Data" }, "children": [ ] }, { "childnum": 0, "data": "Saccharum_officinarum_Data", "children": [ ] }, { "childnum": 0, "data": "Schizosaccharomyces_pombe_Data", "children": [ ] }, { "data": "Staphylococcus_aureus_Data (1)", "attr": { "packageList": "AssessORFData", "id": "Staphylococcus_aureus_Data" }, "children": [ ] }, { "childnum": 0, "data": "Sus_scrofa_Data", "children": [ ] }, { "childnum": 0, "data": "Taeniopygia_guttata_Data", "children": [ ] }, { "childnum": 0, "data": "Triticum_aestivum_Data", "children": [ ] }, { "childnum": 0, "data": "Vitis_vinifera_Data", "children": [ ] }, { "childnum": 0, "data": "Xenopus_laevis_Data", "children": [ ] }, { "childnum": 0, "data": "Xenopus_tropicalis_Data", "children": [ ] }, { "childnum": 0, "data": "Zea_mays_Data", "children": [ ] } ] }, { "data": "PackageTypeData (41)", "attr": { "packageList": "clustifyrdatahub,depmap,optimalFlowData,spatialLIBD,TMExplorer", "id": "PackageTypeData" }, "children": [ { "data": "ExperimentHub (39)", "attr": { "packageList": "adductData,benchmarkfdrData2019,biscuiteerData,bodymapRat,celarefData,celldex,chipseqDBData,clustifyrdatahub,curatedAdipoArray,curatedAdipoChIP,curatedMetagenomicData,curatedTCGAData,depmap,DMRcatedata,DropletTestFiles,FieldEffectCrc,FlowSorted.CordBloodCombined.450k,HCAData,HDCytoData,HighlyReplicatedRNASeq,HMP16SData,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,MethylSeqData,MouseGastrulationData,muscData,NanoporeRNASeq,NestLink,PhyloProfileData,pwrEWAS.data,SCATEData,scRNAseq,sesameData,signatureSearchData,SingleCellMultiModal,spatialLIBD,tartare,TENxBUSData", "id": "ExperimentHub" }, "children": [ ] }, { "data": "ImmunoOncologyData (3)", "attr": { "packageList": "HDCytoData,muscData,optimalFlowData", "id": "ImmunoOncologyData" }, "children": [ ] } ] }, { "data": "RepositoryData (94)", "attr": { "packageList": "depmap,JctSeqData,MIGSAdata,mtbls2,OMICsPCAdata,RGMQLlib", "id": "RepositoryData" }, "children": [ { "data": "ArrayExpress (16)", "attr": { "packageList": "ceu1kgv,COHCAPanno,dyebiasexamples,geuvPack,hgu133plus2CellScore,HumanAffyData,kidpack,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,MMDiffBamSubset,PREDAsampledata,rheumaticConditionWOLLBOLD,RNAseqData.HNRNPC.bam.chr14,sampleClassifierData,yri1kgv", "id": "ArrayExpress" }, "children": [ ] }, { "data": "ENCODE (6)", "attr": { "packageList": "ChIC.data,FunciSNP.data,genomationData,LiebermanAidenHiC2009,OMICsPCAdata,WGSmapp", "id": "ENCODE" }, "children": [ ] }, { "data": "GEO (56)", "attr": { "packageList": "Affyhgu133A2Expr,Affyhgu133aExpr,Affyhgu133Plus2Expr,Affymoe4302Expr,airway,blimaTestingData,breastCancerMAINZ,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,ChimpHumanBrainData,ChIPXpressData,cMap2data,COHCAPanno,CopyNeutralIMA,curatedAdipoArray,curatedAdipoChIP,curatedAdipoRNA,curatedBreastData,DvDdata,EatonEtAlChIPseq,ffpeExampleData,fission,gageData,hgu133plus2CellScore,HiCDataHumanIMR90,HumanAffyData,JctSeqData,KEGGandMetacoreDzPathwaysGEO,KEGGdzPathwaysGEO,leukemiasEset,LiebermanAidenHiC2009,LungCancerACvsSCCGEO,M3DExampleData,MAQCsubset,mcsurvdata,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,muscData,PasillaTranscriptExpr,pathprintGEOData,pcxnData,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally,rheumaticConditionWOLLBOLD,RNAseqData.HNRNPC.bam.chr14,SBGNview.data,SingleCellMultiModal,stemHypoxia,TMExplorer,yeastCC", "id": "GEO" }, "children": [ ] }, { "data": "HapMap (13)", "attr": { "packageList": "ceu1kg,ceuhm3,GGdata,GWASdata,hapmap100khind,hapmap100kxba,hapmap500knsp,hapmap500ksty,hapmapsnp5,hapmapsnp6,hmyriB36,ITALICSData,VariantToolsData", "id": "HapMap" }, "children": [ ] }, { "data": "NCI (10)", "attr": { "packageList": "dsQTL,LiebermanAidenHiC2009,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,NCIgraphData,ProData,rcellminerData,RNAseqData.HNRNPC.bam.chr14,SomaticCancerAlterations", "id": "NCI" }, "children": [ ] }, { "data": "PathwayInteractionDatabase (4)", "attr": { "packageList": "FIs,PathNetData,pathprintGEOData,pcxnData", "id": "PathwayInteractionDatabase" }, "children": [ ] }, { "data": "Project1000genomes (5)", "attr": { "packageList": "ceu1kg,dsQTL,FunciSNP.data,SomaticCancerAlterations,WES.1KG.WUGSC", "id": "Project1000genomes" }, "children": [ ] } ] }, { "data": "ReproducibleResearch (22)", "attr": { "packageList": "BloodCancerMultiOmics2017,curatedMetagenomicData,curatedTCGAData,davidTiling,depmap,DmelSGI,FieldEffectCrc,furrowSeg,HarmonizedTCGAData,Hiiragi2013,HMP16SData,HMP2Data,IHWpaper,MIGSAdata,MOFAdata,MSMB,msqc1,NestLink,PhyloProfileData,PtH2O2lipids,RforProteomics,SingleCellMultiModal", "id": "ReproducibleResearch" }, "children": [ ] }, { "data": "SpecimenSource (103)", "attr": { "packageList": "depmap", "id": "SpecimenSource" }, "children": [ { "data": "CellCulture (8)", "attr": { "packageList": "CONFESSdata,depmap,DmelSGI,HD2013SGI,microRNAome,PtH2O2lipids,RNAinteractMAPK,yeastCC", "id": "CellCulture" }, "children": [ ] }, { "data": "Genome (63)", "attr": { "packageList": "Affyhgu133A2Expr,Affyhgu133Plus2Expr,Affymoe4302Expr,aracne.networks,AssessORFData,bcellViper,biscuiteerData,breakpointRdata,breastCancerVDX,bsseqData,CCl4,ChIPexoQualExample,cnvGSAdata,COSMIC.67,davidTiling,depmap,DMRcatedata,DREAM4,dressCheck,dsQTL,ffpeExampleData,fibroEset,fission,FlowSorted.Blood.EPIC,FlowSorted.CordBloodCombined.450k,gaschYHS,geneLenDataBase,genomationData,GeuvadisTranscriptExpr,geuvPack,GGdata,golubEsets,GSE62944,hgu133plus2CellScore,hgu2beta7,HiCDataHumanIMR90,hmyriB36,JctSeqData,leukemiasEset,LiebermanAidenHiC2009,LungCancerLines,MAQCsubsetAFX,MEDIPSData,mitoODEdata,MMAPPR2data,MMDiffBamSubset,NanoporeRNASeq,pasilla,pasillaBamSubset,PasillaTranscriptExpr,pathprintGEOData,RNAseqData.HNRNPC.bam.chr14,seqCNA.annot,sesameData,shinyMethylData,SomatiCAData,SomaticCancerAlterations,TCGAMethylation450k,tcgaWGBSData.hg19,tweeDEseqCountData,WGSmapp,yeastExpData,yeastNagalakshmi", "id": "Genome" }, "children": [ ] }, { "childnum": 0, "data": "Germline", "children": [ ] }, { "data": "Proteome (6)", "attr": { "packageList": "AssessORFData,depmap,MSstatsBioData,pRolocdata,qPLEXdata,ReactomeGSA.data", "id": "Proteome" }, "children": [ ] }, { "childnum": 0, "data": "Somatic", "children": [ ] }, { "data": "StemCell (9)", "attr": { "packageList": "chromstaRData,depmap,gageData,genomationData,MMDiffBamSubset,Mulder2012,PCHiCdata,pRolocdata,stemHypoxia", "id": "StemCell" }, "children": [ ] }, { "data": "Tissue (30)", "attr": { "packageList": "affydata,antiProfilesData,ChimpHumanBrainData,colonCA,COPDSexualDimorphism.data,curatedBreastData,depmap,DonaPLLP2013,FANTOM3and4CAGE,ffpeExampleData,FieldEffectCrc,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,furrowSeg,leukemiasEset,lumiBarnes,M3DExampleData,PREDAsampledata,pwrEWAS.data,rheumaticConditionWOLLBOLD,spatialLIBD,spqnData,stemHypoxia,TimerQuant,tissueTreg,XhybCasneuf", "id": "Tissue" }, "children": [ ] } ] }, { "data": "TechnologyData (266)", "attr": { "packageList": "ELMER.data,MethylAidData,OMICsPCAdata,TCGAbiolinksGUI.data", "id": "TechnologyData" }, "children": [ { "data": "CGHData (4)", "attr": { "packageList": "beta7,breastCancerNKI,dyebiasexamples,PWMEnrich.Hsapiens.background", "id": "CGHData" }, "children": [ ] }, { "data": "FlowCytometryData (7)", "attr": { "packageList": "flowFitExampleData,flowPloidyData,flowWorkspaceData,gatingMLData,HDCytoData,healthyFlowData,optimalFlowData", "id": "FlowCytometryData" }, "children": [ ] }, { "data": "HighThroughputImagingData (4)", "attr": { "packageList": "CONFESSdata,DmelSGI,HD2013SGI,TimerQuant", "id": "HighThroughputImagingData" }, "children": [ ] }, { "data": "MassSpectrometryData (23)", "attr": { "packageList": "adductData,CardinalWorkflows,CluMSIDdata,DAPARdata,faahKO,gcspikelite,metaMSdata,msdata,msPurityData,msqc1,MSstatsBioData,mtbls2,NestLink,plasFIA,ProData,pRolocdata,PtH2O2lipids,qPLEXdata,RforProteomics,RMassBankData,synapterdata,tartare,topdownrdata", "id": "MassSpectrometryData" }, "children": [ { "data": "ImagingMassSpectrometryData (1)", "attr": { "packageList": "CardinalWorkflows", "id": "ImagingMassSpectrometryData" }, "children": [ ] } ] }, { "data": "MicroarrayData (128)", "attr": { "packageList": "ABAData,affycompData,affydata,AffymetrixDataTestFiles,ALLMLL,AmpAffyExample,antiProfilesData,beadarrayExampleData,BeadArrayUseCases,beta7,bladderbatch,blimaTestingData,breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,brgedata,bronchialIL13,cancerdata,ccdata,CCl4,ccTutorial,CellMapperData,ChimpHumanBrainData,CLL,clustifyrdatahub,cMap2data,COHCAPanno,colonCA,ConnectivityMap,CopyNeutralIMA,curatedAdipoArray,curatedBladderData,curatedBreastData,curatedOvarianData,davidTiling,DeSousa2013,DLBCL,DMRcatedata,DrugVsDiseasedata,dyebiasexamples,ecoliLeucine,estrogen,fabiaData,ffpeExampleData,fibroEset,Fletcher2013a,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,frmaExampleData,gageData,geuvPack,geuvStore2,GGdata,GSBenchMark,GWASdata,HarmanData,hgu133abarcodevecs,hgu133plus2barcodevecs,hgu133plus2CellScore,Hiiragi2013,HIVcDNAvantWout03,HumanAffyData,IlluminaDataTestFiles,KEGGdzPathwaysGEO,kidpack,leukemiasEset,lumiBarnes,LungCancerACvsSCCGEO,lydata,mammaPrintData,MAQCsubset,MAQCsubsetAFX,MAQCsubsetILM,mCSEAdata,mcsurvdata,MetaGxBreast,MetaGxOvarian,MetaGxPancreas,MethylAidData,MIGSAdata,minfiData,minfiDataEPIC,mouse4302barcodevecs,mvoutData,pathprintGEOData,pcxnData,pd.atdschip.tiling,pepDat,PREDAsampledata,prostateCancerCamcap,prostateCancerGrasso,prostateCancerStockholm,prostateCancerTaylor,prostateCancerVarambally,pumadata,pwrEWAS.data,rcellminerData,rheumaticConditionWOLLBOLD,RUVnormalizeData,sampleClassifierData,SBGNview.data,serumStimulation,sesameData,seventyGeneData,SNAGEEdata,SpikeIn,SpikeInSubset,stemHypoxia,stjudem,TCGAWorkflowData,timecoursedata,tinesath1probe,waveTilingData,XhybCasneuf,yeastCC", "id": "MicroarrayData" }, "children": [ { "data": "ChipOnChipData (12)", "attr": { "packageList": "breastCancerNKI,ccTutorial,DLBCL,fibroEset,genomationData,Illumina450ProbeVariants.db,leukemiasEset,LiebermanAidenHiC2009,lumiBarnes,rheumaticConditionWOLLBOLD,stjudem,tinesath1cdf", "id": "ChipOnChipData" }, "children": [ ] }, { "childnum": 0, "data": "GenotypingArrayData", "children": [ ] }, { "data": "MethylationArrayData (17)", "attr": { "packageList": "ARRmData,brgedata,COHCAPanno,CopyNeutralIMA,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,mCSEAdata,MethylAidData,minfiData,minfiDataEPIC,pwrEWAS.data,sesameData,TCGAMethylation450k", "id": "MethylationArrayData" }, "children": [ ] }, { "childnum": 0, "data": "MicroRNAArrayData", "children": [ ] }, { "childnum": 0, "data": "mRNAArrayData", "children": [ ] }, { "data": "MultiChannelData (1)", "attr": { "packageList": "rheumaticConditionWOLLBOLD", "id": "MultiChannelData" }, "children": [ ] }, { "data": "OneChannelData (5)", "attr": { "packageList": "breastCancerNKI,breastCancerVDX,pathprintGEOData,pcxnData,yeastCC", "id": "OneChannelData" }, "children": [ ] }, { "childnum": 0, "data": "ProprietaryPlatformsData", "children": [ ] }, { "childnum": 0, "data": "ReversePhaseProteinArrayData", "children": [ ] }, { "data": "TissueMicroarrayData (17)", "attr": { "packageList": "affydata,ChimpHumanBrainData,colonCA,curatedBreastData,ffpeExampleData,FlowSorted.Blood.450k,FlowSorted.Blood.EPIC,FlowSorted.CordBlood.450k,FlowSorted.CordBloodCombined.450k,FlowSorted.CordBloodNorway.450k,FlowSorted.DLPFC.450k,leukemiasEset,PREDAsampledata,pwrEWAS.data,rheumaticConditionWOLLBOLD,stemHypoxia,XhybCasneuf", "id": "TissueMicroarrayData" }, "children": [ ] }, { "data": "TwoChannelData (6)", "attr": { "packageList": "breastCancerUNT,CopyNeutralIMA,dyebiasexamples,HIVcDNAvantWout03,mammaPrintData,pathprintGEOData", "id": "TwoChannelData" }, "children": [ ] } ] }, { "data": "MicrotitrePlateAssayData (4)", "attr": { "packageList": "DmelSGI,facsDorit,HD2013SGI,RNAinteractMAPK", "id": "MicrotitrePlateAssayData" }, "children": [ ] }, { "data": "qPCRData (4)", "attr": { "packageList": "curatedBreastData,Hiiragi2013,miRcompData,seqc", "id": "qPCRData" }, "children": [ ] }, { "data": "SAGEData (1)", "attr": { "packageList": "dyebiasexamples", "id": "SAGEData" }, "children": [ ] }, { "data": "SequencingData (116)", "attr": { "packageList": "airway,alpineData,AneuFinderData,AssessORFData,bodymapRat,breakpointRdata,bsseqData,celldex,cgdv17,chipseqDBData,clustifyrdatahub,curatedAdipoChIP,curatedAdipoRNA,diffloopdata,DMRcatedata,DREAM4,DropletTestFiles,dsQTL,EatonEtAlChIPseq,etec16s,FieldEffectCrc,fission,genomationData,GeuvadisTranscriptExpr,geuvPack,geuvStore2,GGdata,harbChIP,HelloRangesData,HighlyReplicatedRNASeq,HMP16SData,HMP2Data,JASPAR2014,leeBamViews,LiebermanAidenHiC2009,ListerEtAlBSseq,macrophage,MEDIPSData,MetaGxPancreas,MethylSeqData,microRNAome,minionSummaryData,MMAPPR2data,MouseGastrulationData,msd16s,NanoporeRNASeq,nanotubes,NestLink,NGScopyData,oct4,OMICsPCAdata,parathyroidSE,PasillaTranscriptExpr,pathprintGEOData,PCHiCdata,prebsdata,restfulSEData,RNAmodR.Data,RNAseqData.HNRNPC.bam.chr14,RRBSdata,rRDPData,sampleClassifierData,SCLCBam,scRNAseq,seqc,SomatiCAData,spatialLIBD,TBX20BamSubset,tcgaWGBSData.hg19,TENxBrainData,TENxBUSData,TENxPBMCData,tinesath1probe,tissueTreg,TMExplorer,tximportData,VariantToolsData,WES.1KG.WUGSC,WGSmapp,yeastNagalakshmi,yeastRNASeq", "id": "SequencingData" }, "children": [ { "data": "ChIPSeqData (11)", "attr": { "packageList": "chipseqDBData,chromstaRData,curatedAdipoChIP,EatonEtAlChIPseq,Fletcher2013b,genomationData,LiebermanAidenHiC2009,MMDiffBamSubset,OMICsPCAdata,vulcandata,yeastNagalakshmi", "id": "ChIPSeqData" }, "children": [ ] }, { "data": "DNASeqData (8)", "attr": { "packageList": "breakpointRdata,dsQTL,GSE62944,LiebermanAidenHiC2009,MMDiffBamSubset,pasillaBamSubset,WES.1KG.WUGSC,WGSmapp", "id": "DNASeqData" }, "children": [ ] }, { "childnum": 0, "data": "ExomeSeqData", "children": [ ] }, { "data": "MethylSeqData (1)", "attr": { "packageList": "MethylSeqData", "id": "MethylSeqData" }, "children": [ ] }, { "data": "MicrobiomeData (6)", "attr": { "packageList": "curatedMetagenomicData,etec16s,HMP16SData,HMP2Data,msd16s,rRDPData", "id": "MicrobiomeData" }, "children": [ ] }, { "data": "miRNAData (4)", "attr": { "packageList": "LiebermanAidenHiC2009,microRNAome,rcellminerData,TargetScoreData", "id": "miRNAData" }, "children": [ ] }, { "childnum": 0, "data": "RIPSeqData", "children": [ ] }, { "data": "RNASeqData (56)", "attr": { "packageList": "ABAData,airway,alpineData,benchmarkfdrData2019,bodymapRat,celldex,clustifyrdatahub,curatedAdipoRNA,curatedOvarianData,derfinderData,DropletTestFiles,FieldEffectCrc,fission,GeuvadisTranscriptExpr,GSE62944,GSVAdata,HCAData,HighlyReplicatedRNASeq,HSMMSingleCell,IHWpaper,JctSeqData,leeBamViews,LungCancerLines,M3DExampleData,macrophage,microRNAome,MMAPPR2data,MouseGastrulationData,NanoporeRNASeq,oct4,parathyroidSE,pasilla,pasillaBamSubset,PasillaTranscriptExpr,prebsdata,ReactomeGSA.data,RNAmodR.Data,RNAseqData.HNRNPC.bam.chr14,RnaSeqSampleSizeData,sampleClassifierData,SBGNview.data,scRNAseq,seqc,spqnData,TabulaMurisData,TargetScoreData,TBX20BamSubset,TENxBrainData,TENxPBMCData,timecoursedata,tissueTreg,TMExplorer,tweeDEseqCountData,tximportData,yeastRNASeq,zebrafishRNASeq", "id": "RNASeqData" }, "children": [ ] }, { "childnum": 0, "data": "SangerSeqData", "children": [ ] }, { "data": "SingleCellData (20)", "attr": { "packageList": "benchmarkfdrData2019,breakpointRdata,celarefData,clustifyrdatahub,DropletTestFiles,DuoClustering2018,HCAData,HDCytoData,MouseGastrulationData,muscData,scRNAseq,scTHI.data,SingleCellMultiModal,spatialLIBD,TabulaMurisData,TENxBrainData,TENxBUSData,TENxPBMCData,TMExplorer,WGSmapp", "id": "SingleCellData" }, "children": [ ] }, { "data": "SmallRNAData (1)", "attr": { "packageList": "LiebermanAidenHiC2009", "id": "SmallRNAData" }, "children": [ ] } ] } ] } ] }, { "data": "Workflow (28)", "attr": { "packageList": "annotation,arrays,BiocMetaWorkflow,BP4RNAseq,CAGEWorkflow,chipseqDB,csawUsersGuide,cytofWorkflow,EGSEA123,eQTL,ExpressionNormalizationWorkflow,fluentGenomics,generegulation,highthroughputassays,liftOver,maEndToEnd,methylationArrayAnalysis,proteomics,recountWorkflow,RNAseq123,rnaseqDTU,rnaseqGene,RnaSeqGeneEdgeRQL,sequencing,simpleSingleCell,SingscoreAMLMutations,TCGAWorkflow,variants", "id": "Workflow" }, "children": [ { "data": "AnnotationWorkflow (3)", "attr": { "packageList": "annotation,CAGEWorkflow,variants", "id": "AnnotationWorkflow" }, "children": [ ] }, { "data": "BasicWorkflow (5)", "attr": { "packageList": "arrays,BiocMetaWorkflow,fluentGenomics,liftOver,sequencing", "id": "BasicWorkflow" }, "children": [ ] }, { "childnum": 0, "data": "DifferentialSplicingWorkflow", "children": [ ] }, { "data": "EpigeneticsWorkflow (4)", "attr": { "packageList": "chipseqDB,csawUsersGuide,generegulation,methylationArrayAnalysis", "id": "EpigeneticsWorkflow" }, "children": [ ] }, { "data": "GeneExpressionWorkflow (11)", "attr": { "packageList": "BP4RNAseq,CAGEWorkflow,EGSEA123,ExpressionNormalizationWorkflow,fluentGenomics,maEndToEnd,RNAseq123,rnaseqDTU,rnaseqGene,RnaSeqGeneEdgeRQL,SingscoreAMLMutations", "id": "GeneExpressionWorkflow" }, "children": [ ] }, { "data": "GenomicVariantsWorkflow (2)", "attr": { "packageList": "eQTL,SingscoreAMLMutations", "id": "GenomicVariantsWorkflow" }, "children": [ ] }, { "data": "ImmunoOncologyWorkflow (14)", "attr": { "packageList": "chipseqDB,cytofWorkflow,EGSEA123,ExpressionNormalizationWorkflow,highthroughputassays,proteomics,RNAseq123,rnaseqDTU,rnaseqGene,RnaSeqGeneEdgeRQL,sequencing,simpleSingleCell,SingscoreAMLMutations,variants", "id": "ImmunoOncologyWorkflow" }, "children": [ ] }, { "data": "ProteomicsWorkflow (2)", "attr": { "packageList": "highthroughputassays,proteomics", "id": "ProteomicsWorkflow" }, "children": [ ] }, { "data": "ResourceQueryingWorkflow (2)", "attr": { "packageList": "recountWorkflow,TCGAWorkflow", "id": "ResourceQueryingWorkflow" }, "children": [ ] }, { "data": "SingleCellWorkflow (2)", "attr": { "packageList": "cytofWorkflow,simpleSingleCell", "id": "SingleCellWorkflow" }, "children": [ ] } ] } ]