[ { "data": "Software (936)", "attr": { "packageList": "a4,a4Base,a4Classif,a4Core,a4Preproc,a4Reporting,ABarray,ABSSeq,aCGH,ACME,ADaCGH2,adSplit,affxparser,affy,affycomp,AffyCompatible,affyContam,affycoretools,AffyExpress,affyILM,affyio,affylmGUI,affyPara,affypdnn,affyPLM,affyQCReport,AffyRNADegradation,AffyTiling,AGDEX,agilp,AgiMicroRna,ALDEx2,AllelicImbalance,alsace,altcdfenvs,ampliQueso,annaffy,annmap,annotate,AnnotationDbi,AnnotationForge,AnnotationFuncs,AnnotationHub,annotationTools,anota,antiProfiles,apComplex,aroma.light,ArrayExpress,ArrayExpressHTS,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,ArrayTV,ARRmNormalization,ASEB,ASGSCA,asmn,ASSET,ASSIGN,AtlasRDF,attract,BAC,BADER,BAGS,ballgown,BaseSpaceR,Basic4Cseq,BayesPeak,baySeq,BCRANK,beadarray,beadarraySNP,BeadDataPackR,BEAT,betr,bgafun,BGmix,bgx,BHC,BicARE,BiGGR,bigmemoryExtras,bioassayR,Biobase,BiocCaseStudies,BiocCheck,BiocGenerics,biocGraph,BiocInstaller,BiocParallel,BiocStyle,biocViews,bioDist,biomaRt,BioMVCClass,biomvRCNS,BioNet,BioSeqClass,Biostrings,biosvd,biovizBase,BiRewire,birta,BiSeq,BitSeq,blima,BRAIN,BrainStars,bridge,BridgeDbR,BSgenome,bsseq,BufferedMatrix,BufferedMatrixMethods,bumphunter,BUS,CAFE,CAGEr,CALIB,CAMERA,cancerclass,CancerMutationAnalysis,casper,Category,categoryCompare,ccrepe,cellGrowth,cellHTS,cellHTS2,CellNOptR,CexoR,CFAssay,CGEN,CGHbase,CGHcall,cghMCR,CGHnormaliter,CGHregions,ChAMP,charm,ChemmineOB,ChemmineR,chimera,chipenrich,ChIPpeakAnno,ChIPQC,ChIPseeker,chipseq,ChIPseqR,ChIPsim,ChIPXpress,chopsticks,chroGPS,ChromHeatMap,cisPath,ClassifyR,cleanUpdTSeq,cleaver,clippda,clipper,Clomial,Clonality,clonotypeR,clst,clstutils,clusterProfiler,clusterStab,CMA,cn.farms,cn.mops,CNAnorm,CNEr,CNORdt,CNORfeeder,CNORfuzzy,CNORode,CNTools,cnvGSA,CNVrd2,CNVtools,cobindR,CoCiteStats,codelink,CoGAPS,coGPS,COHCAP,COMPASS,compcodeR,compEpiTools,CompGO,ConsensusClusterPlus,convert,copa,COPDSexualDimorphism,copynumber,CopyNumber450k,CoRegNet,Cormotif,CorMut,coRNAi,CORREP,cosmiq,COSNet,CoverageView,cqn,CRImage,CRISPRseek,crlmm,CSAR,csaw,CSSP,ctc,cummeRbund,customProDB,cycle,dagLogo,daMA,DART,DASiR,DAVIDQuery,DBChIP,ddCt,ddgraph,DECIPHER,DeconRNASeq,DEDS,deepSNV,DEGraph,DEGreport,DEGseq,deltaGseg,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEXSeq,dexus,DFP,DiffBind,diffGeneAnalysis,DirichletMultinomial,dks,DMRcate,DMRforPairs,DNAcopy,DNaseR,domainsignatures,DOQTL,DOSE,DriverNet,DrugVsDisease,DSS,DTA,dualKS,DupChecker,dyebias,DynDoc,EasyqpcR,easyRNASeq,EBarrays,EBcoexpress,EBImage,EBSeq,EBSeqHMM,ecolitk,EDASeq,EDDA,edgeR,eiR,eisa,ELBOW,EnrichmentBrowser,ensemblVEP,ENVISIONQuery,epigenomix,epivizr,erccdashboard,ExiMiR,exomeCopy,exomePeak,explorase,ExpressionView,fabia,facopy,factDesign,farms,fastLiquidAssociation,fastseg,fdrame,FEM,ffpe,FGNet,flagme,flipflop,flowBeads,flowBin,flowcatchR,flowCHIC,flowCL,flowClean,flowClust,flowCore,flowCyBar,flowDensity,flowFit,flowFlowJo,flowFP,flowMap,flowMatch,flowMeans,flowMerge,flowPeaks,flowPhyto,flowPlots,flowQ,flowQB,flowStats,flowTrans,flowType,flowUtils,flowViz,flowWorkspace,fmcsR,focalCall,FourCSeq,FRGEpistasis,frma,frmaTools,FunciSNP,gaga,gage,gaggle,gaia,gaucho,gCMAP,gCMAPWeb,gcrma,gdsfmt,geecc,genArise,GENE.E,GeneAnswers,GeneExpressionSignature,genefilter,genefu,GeneGA,GeneMeta,GeneNetworkBuilder,GeneOverlap,geneplotter,geneRecommender,GeneRegionScan,geneRxCluster,GeneSelectMMD,GeneSelector,geNetClassifier,GeneticsDesign,GeneticsPed,genoCN,GenomeGraphs,GenomeInfoDb,genomeIntervals,genomes,GenomicAlignments,GenomicFeatures,GenomicFiles,GenomicInteractions,GenomicRanges,GenomicTuples,Genominator,genoset,GenoView,GEOmetadb,GEOquery,GEOsubmission,GEWIST,GGBase,ggbio,GGtools,girafe,GLAD,GlobalAncova,globaltest,gmapR,GOexpress,GOFunction,goProfiles,GOSemSim,goseq,GOSim,GOstats,GOsummaries,GOTHiC,goTools,gpls,gprege,graph,GraphAlignment,GraphAT,graphite,GraphPAC,GRENITS,groHMM,GSAR,GSCA,GSEABase,GSEAlm,GSReg,GSRI,GSVA,Gviz,gwascat,GWASTools,h5vc,hapFabia,Harshlight,HCsnip,HDTD,Heatplus,HELP,HEM,hiAnnotator,HilbertVis,HilbertVisGUI,hiReadsProcessor,HiTC,HMMcopy,hopach,hpar,HTqPCR,HTSanalyzeR,HTSeqGenie,htSeqTools,HTSFilter,HybridMTest,hyperdraw,hypergraph,iASeq,iBBiG,ibh,iBMQ,Icens,iChip,iClusterPlus,IdeoViz,idiogram,IdMappingAnalysis,IdMappingRetrieval,illuminaio,imageHTS,IMPCdata,impute,INPower,inSilicoDb,inSilicoMerging,intansv,interactiveDisplay,interactiveDisplayBase,inveRsion,iontree,iPAC,IPPD,IRanges,iSeq,isobar,IsoGeneGUI,ITALICS,iterativeBMA,iterativeBMAsurv,jmosaics,joda,KCsmart,kebabs,KEGGgraph,keggorthology,KEGGprofile,KEGGREST,lapmix,LBE,les,limma,limmaGUI,LiquidAssociation,lmdme,LMGene,logicFS,logitT,lol,LPE,LPEadj,lpNet,lumi,LVSmiRNA,M3D,maanova,macat,maCorrPlot,made4,maigesPack,MAIT,makecdfenv,MANOR,manta,MantelCorr,maPredictDSC,marray,maSigPro,maskBAD,MassArray,massiR,MassSpecWavelet,matchBox,MBAmethyl,MBASED,MBCB,mBPCR,mcaGUI,MCRestimate,mdqc,MeasurementError.cor,MEDIPS,MEDME,MEIGOR,MergeMaid,MeSHDbi,meshr,messina,metaArray,Metab,metabomxtr,metagene,metagenomeSeq,metahdep,metaMS,metaSeq,metaseqR,methVisual,methyAnalysis,MethylAid,MethylMix,methylMnM,methylPipe,MethylSeekR,methylumi,Mfuzz,MGFM,mgsa,MiChip,microRNA,MIMOSA,MineICA,minet,minfi,MinimumDistance,MiPP,MiRaGE,miRNApath,miRNAtap,Mirsynergy,missMethyl,mitoODE,MLInterfaces,MLP,MLSeq,MMDiff,mmnet,MmPalateMiRNA,monocle,MoPS,mosaics,MotifDb,motifRG,motifStack,MotIV,MPFE,mQTL.NMR,MSGFgui,MSGFplus,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,Mulcom,MultiMed,multiscan,multtest,MVCClass,mvGST,mygene,mzID,mzR,NarrowPeaks,ncdfFlow,NCIgraph,neaGUI,nem,netbiov,NetPathMiner,netresponse,NetSAM,networkBMA,NGScopy,nnNorm,NOISeq,nondetects,NormqPCR,npGSEA,NTW,nucleR,nudge,NuPoP,occugene,OCplus,oligo,oligoClasses,OLIN,OLINgui,omicade4,OmicCircos,OncoSimulR,oneChannelGUI,ontoCAT,openCyto,oposSOM,OrderedList,OrganismDbi,OSAT,OTUbase,OutlierD,PAA,PADOG,paircompviz,PAnnBuilder,panp,PANR,PAPi,parody,pathifier,PathNet,pathRender,pathview,paxtoolsr,Pbase,pcaGoPromoter,pcaMethods,pcot2,PCpheno,pdInfoBuilder,pdmclass,PECA,pepStat,pepXMLTab,PGSEA,phenoDist,phenoTest,PhenStat,phyloseq,piano,pickgene,PICS,PING,pint,pkgDepTools,plateCore,plethy,plgem,plier,PLPE,plrs,plw,polyester,Polyfit,ppiStats,prada,prebs,PREDA,predictionet,preprocessCore,proBAMr,PROcess,procoil,ProCoNA,pRoloc,pRolocGUI,PROMISE,prot2D,proteinProfiles,proteoQC,PSEA,PSICQUIC,puma,pvac,pvca,Pviz,PWMEnrich,qcmetrics,QDNAseq,qpcrNorm,qpgraph,qrqc,QUALIFIER,quantro,quantsmooth,QuasR,qusage,qvalue,r3Cseq,R453Plus1Toolbox,rain,rama,RamiGO,randPack,RankProd,Rariant,RbcBook1,RBGL,RBioinf,rBiopaxParser,Rbowtie,rbsurv,Rcade,RCASPAR,Rchemcpp,RchyOptimyx,Rcpi,RCytoscape,RDAVIDWebService,Rdisop,RDRToolbox,ReactomePA,ReadqPCR,reb,RedeR,REDseq,RefNet,RefPlus,regionReport,Repitools,ReportingTools,ReQON,rfPred,rGADEM,RGalaxy,Rgraphviz,RGSEA,rhdf5,rHVDM,riboSeqR,Ringo,RIPSeeker,Risa,RLMM,Rmagpie,RMassBank,rMAT,RmiR,RNAinteract,RNAither,rnaSeqMap,RNASeqPower,Rnits,roar,ROC,Roleswitch,Rolexa,rols,ROntoTools,RPA,RpsiXML,rpx,Rqc,rqubic,rRDP,RRHO,Rsamtools,rsbml,rSFFreader,Rsubread,RSVSim,rTANDEM,RTCA,RTN,RTopper,rtracklayer,Rtreemix,rTRM,rTRMui,RUVnormalize,RUVSeq,RWebServices,S4Vectors,safe,sagenhaft,SAGx,SamSPECTRAL,sangerseqR,SANTA,sapFinder,savR,SBMLR,SCAN.UPC,ScISI,scsR,segmentSeq,SemDist,SeqArray,seqbias,seqCNA,SeqGSEA,seqLogo,seqplots,seqTools,SeqVarTools,SGSeq,shinyMethyl,shinyTANDEM,ShortRead,sigaR,SigCheck,SigFuge,siggenes,sigPathway,SIM,SimBindProfiles,simpleaffy,simulatorZ,sizepower,SJava,SLGI,SLqPCR,SMAP,SNAGEE,snapCGH,snm,SNPchip,SNPRelate,snpStats,SomatiCA,SomaticSignatures,SpacePAC,spade,specL,SpeCond,SPEM,SPIA,spikeLI,spkTools,splicegear,spliceR,spliceSites,SplicingGraphs,splots,spotSegmentation,SQUADD,SRAdb,sRAP,sscore,sSeq,ssize,SSPA,ssviz,STAN,staRank,Starr,STATegRa,stepNorm,stepwiseCM,Streamer,STRINGdb,supraHex,survcomp,Sushi,sva,SwimR,switchBox,synapter,systemPipeR,TargetScore,TargetSearch,TCC,TDARACNE,TEQC,ternarynet,TFBSTools,tigre,tilingArray,timecourse,TitanCNA,tkWidgets,ToPASeq,topGO,tracktables,trackViewer,tRanslatome,TransView,triform,trigger,trio,triplex,TSCAN,tspair,TSSi,TurboNorm,tweeDEseq,twilight,TypeInfo,UNDO,unifiedWMWqPCR,UniProt.ws,VanillaICE,VariantAnnotation,VariantFiltering,VariantTools,vbmp,Vega,VegaMC,viper,vsn,vtpnet,wateRmelon,wavClusteR,waveTiling,weaver,webbioc,widgetTools,xcms,XDE,xmapbridge,xps,XVector,yaqcaffy,zlibbioc", "id": "Software" }, "children": [ { "data": "AssayDomain (299)", "attr": { "packageList": "COPDSexualDimorphism,nondetects", "id": "AssayDomain" }, "children": [ { "data": "aCGH (12)", "attr": { "packageList": "biomvRCNS,Clonality,copynumber,gaia,HCsnip,KCsmart,mBPCR,pint,RCASPAR,sigaR,Vega,VegaMC", "id": "aCGH" }, "children": [ ] }, { "data": "CellBasedAssays (38)", "attr": { "packageList": "bioassayR,cellGrowth,cellHTS,cellHTS2,CellNOptR,CFAssay,ChemmineR,CNORdt,CNORfeeder,CNORode,coRNAi,flowBeads,flowBin,flowCHIC,flowCore,flowCyBar,flowFit,flowFP,flowPlots,flowQ,flowStats,flowUtils,flowViz,fmcsR,HTSanalyzeR,imageHTS,MIMOSA,mitoODE,PANR,phenoDist,plateCore,prada,QUALIFIER,Rchemcpp,RNAinteract,RNAither,RTCA,staRank", "id": "CellBasedAssays" }, "children": [ ] }, { "data": "ChIPchip (7)", "attr": { "packageList": "ChIPpeakAnno,ChIPXpress,iChip,les,MotIV,rGADEM,Starr", "id": "ChIPchip" }, "children": [ ] }, { "data": "CopyNumberVariation (43)", "attr": { "packageList": "aCGH,ArrayTV,beadarraySNP,biomvRCNS,CGHbase,cghMCR,CGHregions,Clonality,cn.farms,cn.mops,CNAnorm,CNTools,CNVrd2,copynumber,CopyNumber450k,crlmm,DNAcopy,exomeCopy,facopy,fastseg,gaia,genoset,GLAD,HMMcopy,ITALICS,KCsmart,MANOR,mBPCR,MinimumDistance,NGScopy,PREDA,QDNAseq,quantsmooth,reb,seqCNA,SMAP,snapCGH,SNPchip,SomatiCA,TitanCNA,VanillaICE,Vega,VegaMC", "id": "CopyNumberVariation" }, "children": [ ] }, { "data": "CpGIsland (6)", "attr": { "packageList": "HELP,M3D,MEDIPS,MEDME,methylumi,TurboNorm", "id": "CpGIsland" }, "children": [ ] }, { "data": "DNAMethylation (38)", "attr": { "packageList": "ARRmNormalization,asmn,BEAT,BiSeq,bsseq,bumphunter,charm,COHCAP,COPDSexualDimorphism,CopyNumber450k,DMRcate,DMRforPairs,DSS,FEM,HELP,les,lumi,M3D,MassArray,MBAmethyl,MEDIPS,MEDME,methVisual,methyAnalysis,MethylAid,MethylMix,methylMnM,methylPipe,MethylSeekR,methylumi,minfi,missMethyl,MPFE,Repitools,shinyMethyl,TransView,TurboNorm,wateRmelon", "id": "DNAMethylation" }, "children": [ ] }, { "data": "ExonArray (6)", "attr": { "packageList": "limma,oligo,puma,siggenes,snm,xps", "id": "ExonArray" }, "children": [ ] }, { "data": "GeneExpression (131)", "attr": { "packageList": "affycoretools,AffyRNADegradation,AGDEX,ALDEx2,ampliQueso,anota,antiProfiles,ASSIGN,AtlasRDF,attract,BioNet,birta,BitSeq,CAFE,casper,categoryCompare,CoGAPS,compEpiTools,COPDSexualDimorphism,CoRegNet,cummeRbund,DART,ddCt,DEGreport,DEGseq,DESeq2,dexus,DMRcate,DrugVsDisease,DTA,EasyqpcR,easyRNASeq,EBSeqHMM,edgeR,eisa,ELBOW,EnrichmentBrowser,epigenomix,erccdashboard,ExiMiR,ExpressionView,farms,fastLiquidAssociation,ffpe,gage,geecc,GeneExpressionSignature,genefu,GeneGA,GeneMeta,GGtools,GOexpress,goseq,GOstats,GOsummaries,GRENITS,GSCA,GSEABase,GSReg,HCsnip,HDTD,HTqPCR,HybridMTest,iBMQ,interactiveDisplay,interactiveDisplayBase,limma,LiquidAssociation,manta,massiR,MBASED,messina,metaseqR,MethylMix,MGFM,MiRaGE,monocle,Mulcom,netresponse,networkBMA,nondetects,NormqPCR,oligo,oposSOM,pathview,pcaGoPromoter,PECA,piano,pint,plgem,Polyfit,prebs,PREDA,PROMISE,puma,qpcrNorm,qpgraph,RBioinf,Rcade,RCASPAR,ReadqPCR,Repitools,RmiR,rnaSeqMap,Rnits,RPA,Rsubread,RTN,SeqGSEA,sigaR,SigCheck,siggenes,snm,spliceR,spliceSites,SplicingGraphs,sRAP,SSPA,supraHex,survcomp,systemPipeR,tigre,ToPASeq,tRanslatome,TransView,trigger,TSCAN,unifiedWMWqPCR,viper,waveTiling,xps", "id": "GeneExpression" }, "children": [ ] }, { "data": "GeneticVariability (23)", "attr": { "packageList": "beadarraySNP,chopsticks,Clomial,CNVtools,deepSNV,DOQTL,FRGEpistasis,GGtools,GSReg,GWASTools,hapFabia,missMethyl,phyloseq,qpgraph,RLMM,Rsubread,RTN,SeqVarTools,SNPchip,snpStats,trigger,trio,VariantTools", "id": "GeneticVariability" }, "children": [ ] }, { "data": "SNP (40)", "attr": { "packageList": "beadarraySNP,BSgenome,CGEN,chopsticks,CNVrd2,copynumber,crlmm,deepSNV,DOQTL,gaucho,GeneRegionScan,GenomicAlignments,genoset,GGtools,GWASTools,hapFabia,iASeq,iBMQ,INPower,inveRsion,logicFS,MassArray,mBPCR,MinimumDistance,oligo,qpgraph,RLMM,Rsubread,RTN,sangerseqR,sapFinder,SeqVarTools,siggenes,SNPchip,snpStats,systemPipeR,trigger,trio,VariantAnnotation,VariantFiltering", "id": "SNP" }, "children": [ ] }, { "data": "Transcription (47)", "attr": { "packageList": "altcdfenvs,ampliQueso,annmap,BAC,BicARE,birta,BitSeq,CAGEr,casper,CexoR,CoRegNet,CSAR,DBChIP,DNaseR,DTA,edgeR,erccdashboard,ExiMiR,geecc,GOexpress,goseq,GSRI,jmosaics,les,limma,MBASED,mosaics,motifRG,NarrowPeaks,netresponse,qpgraph,Rcade,regionReport,rHVDM,rnaSeqMap,roar,RRHO,rTRM,rTRMui,SGSeq,simpleaffy,snm,splicegear,spliceR,tigre,TransView,xps", "id": "Transcription" }, "children": [ ] } ] }, { "data": "BiologicalQuestion (261)", "attr": { "packageList": "geecc,OncoSimulR", "id": "BiologicalQuestion" }, "children": [ { "data": "AlternativeSplicing (7)", "attr": { "packageList": "BitSeq,edgeR,erccdashboard,limma,puma,SGSeq,spliceR", "id": "AlternativeSplicing" }, "children": [ ] }, { "data": "Coverage (13)", "attr": { "packageList": "chipseq,CNAnorm,CNVrd2,compEpiTools,csaw,edgeR,GenomicAlignments,GenomicRanges,M3D,methylPipe,regionReport,Rsamtools,systemPipeR", "id": "Coverage" }, "children": [ ] }, { "childnum": 0, "data": "DemethylateRegionDetection", "children": [ ] }, { "childnum": 0, "data": "DenovoAssembler", "children": [ ] }, { "data": "DifferentialExpression (164)", "attr": { "packageList": "ABSSeq,AffyExpress,affylmGUI,AgiMicroRna,ALDEx2,ampliQueso,anota,ArrayTools,AtlasRDF,BADER,ballgown,baySeq,betr,BGmix,bgx,BioNet,BitSeq,bridge,casper,clippda,coGPS,compcodeR,copa,COPDSexualDimorphism,Cormotif,cqn,cummeRbund,daMA,DART,ddCt,DeconRNASeq,DEDS,DEGraph,DEGreport,DEGseq,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEXSeq,dexus,DFP,diffGeneAnalysis,DMRcate,DSS,DTA,EBarrays,EBSeq,EBSeqHMM,EDASeq,edgeR,EnrichmentBrowser,epigenomix,erccdashboard,fabia,factDesign,fdrame,FEM,flagme,gaga,gage,genefu,GeneSelectMMD,GeneSelector,geNetClassifier,GlobalAncova,globaltest,GOexpress,gprege,GSAR,GSRI,HDTD,HEM,HTqPCR,HTSFilter,IsoGeneGUI,lapmix,les,limma,limmaGUI,lmdme,LMGene,logitT,LPE,maanova,macat,maigesPack,manta,maSigPro,MEDIPS,MergeMaid,messina,metaArray,metagenomeSeq,metahdep,metaSeq,metaseqR,MethylMix,miRNApath,MmPalateMiRNA,monocle,Mulcom,multtest,mvGST,neaGUI,netresponse,NOISeq,nudge,OCplus,oligo,oneChannelGUI,oposSOM,OrderedList,PathNet,pathview,pcot2,PECA,phenoTest,piano,pickgene,pint,plgem,PLPE,plw,polyester,Polyfit,prot2D,puma,RankProd,Rcade,RDAVIDWebService,regionReport,rnaSeqMap,Rnits,ROC,RUVSeq,safe,SAGx,segmentSeq,SeqGSEA,sigaR,siggenes,sigPathway,simpleaffy,snm,SpeCond,spliceR,spliceSites,sRAP,sscore,ssize,survcomp,TCC,timecourse,ToPASeq,tRanslatome,tweeDEseq,twilight,unifiedWMWqPCR,waveTiling,webbioc,XDE,xps", "id": "DifferentialExpression" }, "children": [ ] }, { "data": "DifferentialMethylation (7)", "attr": { "packageList": "COHCAP,DMRcate,DMRforPairs,FEM,M3D,MethylMix,missMethyl", "id": "DifferentialMethylation" }, "children": [ ] }, { "data": "DifferentialPeakCalling (1)", "attr": { "packageList": "DiffBind", "id": "DifferentialPeakCalling" }, "children": [ ] }, { "data": "DifferentialSplicing (6)", "attr": { "packageList": "BitSeq,edgeR,erccdashboard,limma,puma,spliceR", "id": "DifferentialSplicing" }, "children": [ ] }, { "childnum": 0, "data": "DriverMutation", "children": [ ] }, { "data": "FunctionalPrediction (1)", "attr": { "packageList": "viper", "id": "FunctionalPrediction" }, "children": [ ] }, { "childnum": 0, "data": "GeneFusionDetection", "children": [ ] }, { "childnum": 0, "data": "GenePrediction", "children": [ ] }, { "data": "GeneRegulation (21)", "attr": { "packageList": "BCRANK,cleanUpdTSeq,CNEr,CoRegNet,CRISPRseek,FEM,GRENITS,GSReg,GSRI,MethylMix,MoPS,qpgraph,Rsubread,RTN,rTRM,rTRMui,TFBSTools,tigre,tRanslatome,triplex,viper", "id": "GeneRegulation" }, "children": [ ] }, { "data": "GeneSetEnrichment (41)", "attr": { "packageList": "AtlasRDF,CAFE,Category,chipenrich,clusterProfiler,CompGO,domainsignatures,DOSE,edgeR,EnrichmentBrowser,facopy,FGNet,gage,gCMAPWeb,geecc,GOexpress,GOFunction,GOstats,GSEABase,GSReg,GSRI,GSVA,iBBiG,limma,mgsa,mvGST,npGSEA,oposSOM,pathview,paxtoolsr,piano,qusage,ReactomePA,ReportingTools,RGSEA,RTN,safe,SeqGSEA,SigCheck,sRAP,systemPipeR", "id": "GeneSetEnrichment" }, "children": [ ] }, { "childnum": 0, "data": "GeneSignaling", "children": [ ] }, { "data": "GeneTarget (1)", "attr": { "packageList": "networkBMA", "id": "GeneTarget" }, "children": [ ] }, { "data": "GenomeAnnotation (10)", "attr": { "packageList": "AnnotationDbi,compEpiTools,DMRcate,GenomeInfoDb,GenomicFeatures,GenomicRanges,microRNA,QDNAseq,Rsubread,STAN", "id": "GenomeAnnotation" }, "children": [ ] }, { "childnum": 0, "data": "GenomeAssembly", "children": [ ] }, { "childnum": 0, "data": "GenomeWideAssociation", "children": [ ] }, { "data": "GenomicVariation (6)", "attr": { "packageList": "CNAnorm,facopy,missMethyl,Rariant,SomaticSignatures,TitanCNA", "id": "GenomicVariation" }, "children": [ ] }, { "childnum": 0, "data": "GermlineMutation", "children": [ ] }, { "childnum": 0, "data": "HistoneModification", "children": [ ] }, { "childnum": 0, "data": "IndelDetection", "children": [ ] }, { "data": "LinkageDisequilibrium (1)", "attr": { "packageList": "CNVrd2", "id": "LinkageDisequilibrium" }, "children": [ ] }, { "childnum": 0, "data": "MetagenomeAssembly", "children": [ ] }, { "childnum": 0, "data": "MicrosatelliteDetection", "children": [ ] }, { "data": "MotifAnnotation (3)", "attr": { "packageList": "MotifDb,MotIV,TFBSTools", "id": "MotifAnnotation" }, "children": [ ] }, { "data": "MotifDiscovery (4)", "attr": { "packageList": "BCRANK,motifRG,rGADEM,TFBSTools", "id": "MotifDiscovery" }, "children": [ ] }, { "data": "NetworkEnrichment (13)", "attr": { "packageList": "BioNet,CoRegNet,DEGraph,EnrichmentBrowser,FEM,FGNet,ibh,miRNApath,paxtoolsr,RTN,SANTA,ToPASeq,viper", "id": "NetworkEnrichment" }, "children": [ ] }, { "data": "NetworkInference (17)", "attr": { "packageList": "apComplex,CNORfeeder,CoRegNet,FRGEpistasis,GRENITS,joda,minet,networkBMA,PANR,ppiStats,predictionet,qpgraph,rHVDM,RTN,ScISI,SPEM,tigre", "id": "NetworkInference" }, "children": [ ] }, { "childnum": 0, "data": "NucleosomePositioning", "children": [ ] }, { "childnum": 0, "data": "PeakDetection", "children": [ ] }, { "childnum": 0, "data": "QuantitativeTrailLocus", "children": [ ] }, { "childnum": 0, "data": "Scaffolding", "children": [ ] }, { "data": "SequenceMatching (17)", "attr": { "packageList": "Biostrings,BSgenome,cleanUpdTSeq,cobindR,CRISPRseek,dagLogo,FunciSNP,hapFabia,microRNA,MmPalateMiRNA,motifStack,PWMEnrich,REDseq,RRHO,Rsubread,seqLogo,triplex", "id": "SequenceMatching" }, "children": [ ] }, { "data": "SomaticMutation (4)", "attr": { "packageList": "gaucho,OncoSimulR,Rariant,SomaticSignatures", "id": "SomaticMutation" }, "children": [ ] }, { "childnum": 0, "data": "SplicedAlignment", "children": [ ] }, { "childnum": 0, "data": "StructuralVariation", "children": [ ] }, { "childnum": 0, "data": "TranscriptomeVariant", "children": [ ] }, { "childnum": 0, "data": "VariantAnnotation", "children": [ ] }, { "data": "VariantDetection (1)", "attr": { "packageList": "Rariant", "id": "VariantDetection" }, "children": [ ] } ] }, { "data": "Infrastructure (187)", "attr": { "packageList": "affxparser,AffyCompatible,affyContam,affyio,AllelicImbalance,AnnotationForge,AnnotationHub,aroma.light,arrayMvout,BaseSpaceR,bigmemoryExtras,bioassayR,Biobase,BiocCaseStudies,BiocCheck,BiocGenerics,BiocParallel,biocViews,BioMVCClass,Biostrings,biovizBase,BSgenome,BufferedMatrix,BufferedMatrixMethods,bumphunter,CGHbase,ChemmineR,chimera,ChIPseqR,ChIPsim,convert,cummeRbund,DynDoc,eiR,epivizr,flowBeads,flowcatchR,flowCore,flowQ,flowUtils,flowViz,fmcsR,FunciSNP,gdsfmt,GeneAnswers,genomeIntervals,GenomicAlignments,GenomicFeatures,GenomicFiles,GenomicInteractions,GenomicRanges,GenomicTuples,Genominator,genoset,GEOmetadb,GGBase,ggbio,Icens,illuminaio,IRanges,MeSHDbi,microRNA,monocle,MSnbase,MVCClass,mzR,oligoClasses,OrganismDbi,panp,Pbase,pdInfoBuilder,pkgDepTools,plateCore,preprocessCore,QUALIFIER,R453Plus1Toolbox,Rchemcpp,RedeR,RGalaxy,rhdf5,RpsiXML,rRDP,RTCA,RWebServices,S4Vectors,SeqArray,SJava,SNPRelate,splicegear,SRAdb,Streamer,Sushi,systemPipeR,tkWidgets,TypeInfo,UniProt.ws,weaver,webbioc,widgetTools,XVector,zlibbioc", "id": "Infrastructure" }, "children": [ { "data": "DataImport (82)", "attr": { "packageList": "aCGH,affxparser,affyio,affylmGUI,ArrayExpress,AtlasRDF,BaseSpaceR,beadarraySNP,bioassayR,BioNet,Biostrings,BrainStars,cellGrowth,ChemmineR,chipseq,CNEr,codelink,ctc,cummeRbund,DECIPHER,deepSNV,eiR,flowPhyto,flowWorkspace,fmcsR,FunciSNP,gaggle,gdsfmt,GeneRegionScan,genomeIntervals,GenomicAlignments,GenomicFiles,GenomicInteractions,GEOquery,HELP,HTqPCR,ibh,illuminaio,inSilicoDb,limma,limmaGUI,makecdfenv,MANOR,manta,MassArray,minfi,monocle,MSnbase,mzID,mzR,oligo,oneChannelGUI,openCyto,OTUbase,Pbase,plethy,PSICQUIC,puma,qrqc,R453Plus1Toolbox,Rchemcpp,Rcpi,ReadqPCR,rhdf5,Ringo,Risa,Rolexa,rpx,Rsamtools,rSFFreader,rtracklayer,SAGx,segmentSeq,ShortRead,simpleaffy,SRAdb,Starr,Streamer,systemPipeR,TransView,VariantAnnotation,xps", "id": "DataImport" }, "children": [ ] }, { "data": "DataRepresentation (34)", "attr": { "packageList": "AtlasRDF,BaseSpaceR,bigmemoryExtras,Biostrings,BSgenome,cummeRbund,flowPlots,flowWorkspace,FunciSNP,GeneAnswers,GenomeInfoDb,GenomicInteractions,GenomicTuples,genoset,GOexpress,interactiveDisplay,interactiveDisplayBase,IRanges,monocle,ontoCAT,openCyto,oposSOM,OSAT,Pbase,plethy,R453Plus1Toolbox,rBiopaxParser,Rcpi,RedeR,ReportingTools,S4Vectors,SplicingGraphs,Sushi,XVector", "id": "DataRepresentation" }, "children": [ ] }, { "data": "GUI (20)", "attr": { "packageList": "affylmGUI,epivizr,explorase,flowcatchR,gCMAPWeb,GSCA,interactiveDisplay,interactiveDisplayBase,IsoGeneGUI,limmaGUI,mcaGUI,MethylAid,MSGFgui,neaGUI,oneChannelGUI,pRolocGUI,rTRMui,spade,synapter,TSCAN", "id": "GUI" }, "children": [ ] }, { "data": "ThirdPartyClient (9)", "attr": { "packageList": "gaggle,GENE.E,graphite,KEGGREST,maigesPack,PSICQUIC,RamiGO,RCytoscape,rpx", "id": "ThirdPartyClient" }, "children": [ ] } ] }, { "data": "ResearchField (193)", "attr": { "packageList": "aCGH,AGDEX,AllelicImbalance,ASEB,BaseSpaceR,BEAT,BiGGR,bioassayR,biomvRCNS,Biostrings,BiSeq,BRAIN,BSgenome,CancerMutationAnalysis,ccrepe,CellNOptR,CellNOptR,CexoR,CFAssay,ChemmineOB,ChemmineR,cisPath,cleanUpdTSeq,cleaver,clippda,Clomial,cn.mops,cn.mops,CNORdt,CNORdt,CNORfeeder,CNORfeeder,CNORode,CNORode,cobindR,copynumber,CoRegNet,cosmiq,CRImage,CSAR,csaw,customProDB,DBChIP,DECIPHER,deepSNV,deltaGseg,dexus,DMRcate,DNaseR,DOQTL,easyRNASeq,edgeR,eiR,erccdashboard,exomeCopy,facopy,fastLiquidAssociation,fastLiquidAssociation,FEM,FGNet,flowcatchR,flowDensity,flowMeans,fmcsR,FRGEpistasis,gage,gage,gaucho,GeneMeta,geneRxCluster,GeneticsDesign,GeneticsPed,genoCN,GenomeInfoDb,genomeIntervals,genomes,GenomicAlignments,GenomicFeatures,GenomicRanges,GEWIST,GGBase,GGtools,GOexpress,GraphPAC,gwascat,hapFabia,HDTD,hpar,hpar,HybridMTest,intansv,interactiveDisplay,interactiveDisplayBase,iontree,iPAC,IPPD,isobar,jmosaics,limma,LiquidAssociation,LiquidAssociation,logicFS,LPEadj,MAIT,manta,MassArray,MassSpecWavelet,MEIGOR,messina,Metab,metabomxtr,metagene,metagenomeSeq,metaMS,MGFM,MLP,mmnet,mosaics,mQTL.NMR,MSGFgui,MSGFplus,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,mzID,mzR,mzR,NarrowPeaks,netresponse,netresponse,nucleR,NuPoP,PAA,PAnnBuilder,PAPi,pathview,pathview,pathview,pathview,paxtoolsr,Pbase,PCpheno,pepXMLTab,phyloseq,pint,plgem,PLPE,ppiStats,PREDA,proBAMr,PROcess,procoil,ProCoNA,pRoloc,pRolocGUI,prot2D,proteoQC,Pviz,qcmetrics,QDNAseq,qpgraph,QuasR,rain,rain,rain,Rcade,RCASPAR,RCASPAR,Rchemcpp,Rcpi,Rcpi,Rcpi,Rcpi,riboSeqR,RMassBank,RpsiXML,rpx,rRDP,RRHO,Rsubread,rTANDEM,SamSPECTRAL,sapFinder,ScISI,SeqArray,seqCNA,SeqVarTools,shinyTANDEM,SLGI,SLGI,SNPRelate,SpacePAC,specL,spliceSites,SplicingGraphs,ssviz,staRank,Sushi,synapter,systemPipeR,TEQC,ternarynet,TitanCNA,tRanslatome,trigger,trio,TSSi,VariantAnnotation,VariantFiltering,VariantTools,viper,xcms", "id": "ResearchField" }, "children": [ { "childnum": 0, "data": "Agroinformatics", "children": [ ] }, { "data": "BiomedicalInformatics (2)", "attr": { "packageList": "messina,Rcpi", "id": "BiomedicalInformatics" }, "children": [ ] }, { "childnum": 0, "data": "Biophysics", "children": [ ] }, { "data": "CellBiology (20)", "attr": { "packageList": "CellNOptR,CFAssay,cn.mops,CNORdt,CNORfeeder,CNORode,cobindR,CRImage,dexus,fastLiquidAssociation,flowcatchR,flowDensity,flowMeans,hpar,LiquidAssociation,netresponse,SamSPECTRAL,staRank,ternarynet,tRanslatome", "id": "CellBiology" }, "children": [ ] }, { "data": "Cheminformatics (3)", "attr": { "packageList": "ChemmineOB,mQTL.NMR,Rcpi", "id": "Cheminformatics" }, "children": [ ] }, { "childnum": 0, "data": "ComparativeGenomics", "children": [ ] }, { "childnum": 0, "data": "ComputationalChemistry", "children": [ ] }, { "data": "FunctionalGenomics (1)", "attr": { "packageList": "FGNet", "id": "FunctionalGenomics" }, "children": [ ] }, { "data": "Genetics (96)", "attr": { "packageList": "aCGH,AGDEX,AllelicImbalance,BaseSpaceR,BEAT,biomvRCNS,Biostrings,BiSeq,BSgenome,CancerMutationAnalysis,CexoR,cleanUpdTSeq,Clomial,cn.mops,copynumber,CSAR,csaw,DBChIP,DECIPHER,deepSNV,DMRcate,DNaseR,DOQTL,easyRNASeq,edgeR,erccdashboard,exomeCopy,facopy,fastLiquidAssociation,FRGEpistasis,gage,gaucho,geneRxCluster,GeneticsDesign,GeneticsPed,genoCN,GenomeInfoDb,genomeIntervals,genomes,GenomicAlignments,GenomicFeatures,GenomicRanges,GEWIST,GGBase,GGtools,gwascat,hapFabia,HDTD,HybridMTest,intansv,interactiveDisplay,interactiveDisplayBase,jmosaics,limma,LiquidAssociation,logicFS,manta,MassArray,metagene,MGFM,MLP,mosaics,NarrowPeaks,netresponse,nucleR,NuPoP,pathview,pint,PREDA,QDNAseq,qpgraph,QuasR,rain,Rcade,RCASPAR,riboSeqR,rRDP,RRHO,Rsubread,SeqArray,seqCNA,SeqVarTools,SLGI,SNPRelate,SplicingGraphs,ssviz,Sushi,systemPipeR,TEQC,TitanCNA,trigger,trio,TSSi,VariantAnnotation,VariantFiltering,VariantTools", "id": "Genetics" }, "children": [ ] }, { "childnum": 0, "data": "Lipidomics", "children": [ ] }, { "childnum": 0, "data": "MathematicalBiology", "children": [ ] }, { "data": "Metabolomics (12)", "attr": { "packageList": "BiGGR,cosmiq,iontree,MAIT,Metab,metabomxtr,metaMS,mzR,PAPi,pathview,RMassBank,xcms", "id": "Metabolomics" }, "children": [ ] }, { "data": "Metagenomics (5)", "attr": { "packageList": "ccrepe,GeneMeta,GOexpress,metagenomeSeq,phyloseq", "id": "Metagenomics" }, "children": [ ] }, { "childnum": 0, "data": "Pharmacogenetics", "children": [ ] }, { "childnum": 0, "data": "Pharmacogenomics", "children": [ ] }, { "data": "Proteomics (65)", "attr": { "packageList": "ASEB,bioassayR,BRAIN,CellNOptR,ChemmineR,cisPath,cleaver,clippda,CNORdt,CNORfeeder,CNORode,customProDB,deltaGseg,eiR,fmcsR,GraphPAC,hpar,iPAC,IPPD,isobar,LPEadj,MassSpecWavelet,MSGFgui,MSGFplus,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,mzID,mzR,PAA,PAnnBuilder,pathview,Pbase,PCpheno,pepXMLTab,plgem,PLPE,ppiStats,proBAMr,PROcess,procoil,ProCoNA,pRoloc,pRolocGUI,prot2D,proteoQC,Pviz,qcmetrics,rain,RCASPAR,Rchemcpp,Rcpi,RpsiXML,rpx,rTANDEM,sapFinder,ScISI,shinyTANDEM,SLGI,SpacePAC,specL,spliceSites,synapter", "id": "Proteomics" }, "children": [ ] }, { "childnum": 0, "data": "StructuralGenomics", "children": [ ] }, { "data": "SystemsBiology (10)", "attr": { "packageList": "CoRegNet,FEM,gage,MEIGOR,mmnet,pathview,paxtoolsr,rain,Rcpi,viper", "id": "SystemsBiology" }, "children": [ ] } ] }, { "data": "StatisticalMethod (261)", "attr": { "packageList": "agilp,ArrayTools,attract,ballgown,EBSeq,EBSeqHMM,fabia,geecc,GeneSelector,GSAR,HDTD,joda,lol,MeasurementError.cor,MethylMix,Mulcom,MultiMed,npGSEA,OmicCircos,oneChannelGUI,PING,randPack,Rariant,RGSEA,Rtreemix,RUVnormalize,safe,SNPRelate,SomaticSignatures,SSPA,STATegRa,sva,switchBox,TitanCNA,tweeDEseq", "id": "StatisticalMethod" }, "children": [ { "data": "Bayesian (15)", "attr": { "packageList": "ALDEx2,ASSIGN,BAGS,BitSeq,Clomial,CSSP,EBcoexpress,EBSeqHMM,edgeR,GRENITS,limma,networkBMA,pcaMethods,puma,tigre", "id": "Bayesian" }, "children": [ ] }, { "data": "Classification (65)", "attr": { "packageList": "antiProfiles,bgafun,bioDist,BioSeqClass,cancerclass,ClassifyR,Clonality,clst,clstutils,CMA,COSNet,CRImage,ctc,dexus,DirichletMultinomial,dualKS,eisa,epigenomix,ExpressionView,fastseg,flowcatchR,flowPhyto,gaga,genefu,geNetClassifier,gpls,interactiveDisplay,interactiveDisplayBase,iterativeBMA,kebabs,logicFS,made4,maigesPack,maPredictDSC,massiR,MCRestimate,messina,methVisual,MiPP,miRNAtap,MLInterfaces,MLSeq,MoPS,NetPathMiner,NuPoP,omicade4,ontoCAT,PAA,pdmclass,phenoTest,phyloseq,procoil,pRoloc,RamiGO,RBioinf,rfPred,RGSEA,rHVDM,Rmagpie,rRDP,SemDist,SigCheck,stepwiseCM,switchBox,vbmp", "id": "Classification" }, "children": [ ] }, { "data": "Clustering (89)", "attr": { "packageList": "adSplit,BHC,BicARE,bioDist,CAGEr,CGEN,ChemmineR,chroGPS,Clomial,clusterProfiler,clusterStab,ConsensusClusterPlus,CORREP,ctc,cummeRbund,DECIPHER,deltaGseg,DirichletMultinomial,DrugVsDisease,EBarrays,edgeR,eiR,fabia,FGNet,flowCHIC,flowClust,flowCyBar,flowDensity,flowFP,flowMatch,flowMeans,flowMerge,flowPeaks,flowPhyto,fmcsR,genefu,geneRecommender,geneRxCluster,GOexpress,GOSemSim,GOSim,GOsummaries,GraphPAC,hapFabia,HCsnip,hopach,iBBiG,iClusterPlus,iPAC,kebabs,limma,maanova,made4,maigesPack,MantelCorr,massiR,mcaGUI,methVisual,Mfuzz,Mirsynergy,MLInterfaces,MLSeq,MmPalateMiRNA,monocle,NetPathMiner,netresponse,omicade4,PANR,phenoTest,phyloseq,PICS,PING,pRoloc,puma,RBioinf,Rchemcpp,RDRToolbox,rqubic,SAGx,SamSPECTRAL,SANTA,SigFuge,SomaticSignatures,SpacePAC,spade,SpeCond,STATegRa,supraHex,TransView", "id": "Clustering" }, "children": [ ] }, { "data": "DecisionTree (7)", "attr": { "packageList": "CMA,DEGraph,flowUtils,GOSim,nem,ScISI,TargetSearch", "id": "DecisionTree" }, "children": [ ] }, { "data": "DimensionReduction (2)", "attr": { "packageList": "RDRToolbox,STATegRa", "id": "DimensionReduction" }, "children": [ ] }, { "data": "FeatureExtraction (2)", "attr": { "packageList": "Rcpi,RDRToolbox", "id": "FeatureExtraction" }, "children": [ ] }, { "data": "GraphAndNetwork (69)", "attr": { "packageList": "apComplex,biocGraph,BioMVCClass,BioNet,birta,CoRegNet,CORREP,COSNet,DART,ddgraph,DEGraph,EnrichmentBrowser,gaggle,GeneNetworkBuilder,GOstats,graph,GraphAlignment,GraphAT,graphite,GRENITS,GSEABase,hyperdraw,hypergraph,ibh,joda,KEGGgraph,keggorthology,maigesPack,minet,MVCClass,mvGST,NCIgraph,nem,netbiov,NetPathMiner,netresponse,paircompviz,PANR,pathRender,pathview,paxtoolsr,PCpheno,pkgDepTools,ppiStats,predictionet,ProCoNA,PSICQUIC,qpgraph,RamiGO,RBGL,Rcpi,RCytoscape,RDAVIDWebService,RedeR,RefNet,Rgraphviz,rHVDM,rsbml,RTN,rTRM,rTRMui,SBMLR,ScISI,SLGI,spade,SPIA,SQUADD,ternarynet,ToPASeq", "id": "GraphAndNetwork" }, "children": [ ] }, { "data": "HiddenMarkovModel (4)", "attr": { "packageList": "DOQTL,EBSeqHMM,STAN,TitanCNA", "id": "HiddenMarkovModel" }, "children": [ ] }, { "childnum": 0, "data": "MultidimensionalScaling", "children": [ ] }, { "data": "NeuralNetwork (1)", "attr": { "packageList": "COSNet", "id": "NeuralNetwork" }, "children": [ ] }, { "childnum": 0, "data": "PatternLogic", "children": [ ] }, { "data": "PrincipalComponent (2)", "attr": { "packageList": "SNPRelate,STATegRa", "id": "PrincipalComponent" }, "children": [ ] }, { "data": "Regression (7)", "attr": { "packageList": "CFAssay,edgeR,gpls,kebabs,limma,MoPS,plrs", "id": "Regression" }, "children": [ ] }, { "data": "StructuralEquationModels (1)", "attr": { "packageList": "ASGSCA", "id": "StructuralEquationModels" }, "children": [ ] }, { "data": "SupportVectorMachine (1)", "attr": { "packageList": "kebabs", "id": "SupportVectorMachine" }, "children": [ ] }, { "data": "Survival (4)", "attr": { "packageList": "CFAssay,ClassifyR,messina,simulatorZ", "id": "Survival" }, "children": [ ] }, { "data": "TimeCourse (29)", "attr": { "packageList": "betr,biosvd,cellGrowth,CellNOptR,CNORdt,CNORode,cycle,deltaGseg,DMRcate,EBSeqHMM,edgeR,GOexpress,gprege,GRENITS,limma,LiquidAssociation,maSigPro,Mfuzz,mitoODE,MoPS,plethy,rain,RmiR,Rnits,RTCA,TDARACNE,tigre,timecourse,waveTiling", "id": "TimeCourse" }, "children": [ ] } ] }, { "data": "Technology (591)", "attr": { "packageList": "ACME,CoverageView,ELBOW,nondetects,spkTools", "id": "Technology" }, "children": [ { "data": "FlowCytometry (36)", "attr": { "packageList": "COMPASS,flowBeads,flowBin,flowCHIC,flowCL,flowClean,flowClust,flowCore,flowCyBar,flowDensity,flowFit,flowFlowJo,flowFP,flowMap,flowMatch,flowMeans,flowMerge,flowPeaks,flowPhyto,flowPlots,flowQ,flowQB,flowStats,flowTrans,flowType,flowUtils,flowViz,flowWorkspace,MIMOSA,ncdfFlow,openCyto,plateCore,QUALIFIER,RchyOptimyx,SamSPECTRAL,spade", "id": "FlowCytometry" }, "children": [ ] }, { "data": "MassSpectrometry (44)", "attr": { "packageList": "apComplex,BRAIN,CAMERA,cosmiq,flagme,gaga,iontree,isobar,MAIT,MassArray,MassSpecWavelet,Metab,metabomxtr,metaMS,MSGFgui,MSGFplus,msmsEDA,msmsTests,MSnbase,MSnID,MSstats,mzID,mzR,PAPi,Pbase,pepXMLTab,plgem,proBAMr,PROcess,pRoloc,proteoQC,qcmetrics,Rdisop,Risa,RMassBank,rols,rpx,rTANDEM,sapFinder,shinyTANDEM,specL,synapter,TargetSearch,xcms", "id": "MassSpectrometry" }, "children": [ { "childnum": 0, "data": "ImagingMassSpectrometry", "children": [ ] } ] }, { "data": "Microarray (328)", "attr": { "packageList": "a4,a4Base,a4Classif,a4Core,a4Preproc,a4Reporting,ABarray,ACME,ADaCGH2,adSplit,affy,affycomp,AffyCompatible,affycoretools,AffyExpress,affyILM,affyio,affylmGUI,affyPara,affypdnn,affyPLM,affyQCReport,AffyRNADegradation,AffyTiling,AGDEX,AgiMicroRna,altcdfenvs,annaffy,annmap,AnnotationDbi,annotationTools,anota,aroma.light,ArrayExpress,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,ARRmNormalization,AtlasRDF,BAC,beadarray,BeadDataPackR,betr,BGmix,bgx,BHC,BicARE,biomvRCNS,BioNet,birta,blima,BrainStars,bridge,CAFE,CALIB,cancerclass,CGHbase,CGHcall,cghMCR,CGHnormaliter,CGHregions,ChAMP,charm,chopsticks,Clonality,cn.farms,CNTools,codelink,CoGAPS,coGPS,COHCAP,convert,COPDSexualDimorphism,CopyNumber450k,Cormotif,CORREP,crlmm,ctc,cycle,daMA,DECIPHER,DEDS,DEGraph,DFP,diffGeneAnalysis,DMRcate,DMRforPairs,DNAcopy,DrugVsDisease,DTA,dualKS,dyebias,eisa,ELBOW,EnrichmentBrowser,erccdashboard,ExiMiR,explorase,ExpressionView,fabia,facopy,factDesign,farms,fdrame,ffpe,focalCall,frma,frmaTools,gage,gCMAP,gcrma,geecc,genArise,genefilter,GeneMeta,GeneNetworkBuilder,geneRecommender,GeneRegionScan,geNetClassifier,genoCN,GenomeGraphs,genoset,GEOquery,GEOsubmission,GLAD,GlobalAncova,globaltest,GOexpress,GOFunction,goProfiles,GOstats,goTools,gpls,gprege,GSEAlm,GSRI,GSVA,Gviz,GWASTools,Harshlight,HCsnip,HDTD,Heatplus,HELP,HEM,HMMcopy,HybridMTest,iBMQ,iChip,iClusterPlus,IdeoViz,impute,inSilicoDb,inSilicoMerging,interactiveDisplay,interactiveDisplayBase,inveRsion,IsoGeneGUI,ITALICS,iterativeBMA,iterativeBMAsurv,joda,KCsmart,lapmix,les,limma,limmaGUI,lmdme,LMGene,logitT,LPE,LPEadj,lumi,LVSmiRNA,maanova,macat,maCorrPlot,maigesPack,MANOR,maPredictDSC,marray,maSigPro,maskBAD,massiR,matchBox,MBCB,mBPCR,mdqc,MEDME,MergeMaid,metaArray,metahdep,methyAnalysis,MethylAid,Mfuzz,MGFM,MiChip,minet,minfi,MinimumDistance,MiPP,MiRaGE,miRNAtap,MmPalateMiRNA,MotIV,Mulcom,multiscan,multtest,mvGST,neaGUI,nem,netresponse,nnNorm,npGSEA,nucleR,nudge,OCplus,oligo,OLIN,OLINgui,oneChannelGUI,OrderedList,OutlierD,PAA,PADOG,pathview,pcaGoPromoter,pcot2,PECA,pepStat,PGSEA,phenoTest,piano,pickgene,pint,plgem,PLPE,plw,prebs,PROMISE,puma,pvac,pvca,Pviz,qcmetrics,qpgraph,quantro,qusage,rain,rama,RBioinf,rbsurv,RDRToolbox,reb,RefPlus,ReportingTools,rGADEM,rHVDM,Ringo,RLMM,Rmagpie,rMAT,RmiR,Rnits,ROntoTools,RPA,rqubic,RRHO,RTopper,SAGx,SCAN.UPC,shinyMethyl,sigaR,siggenes,SIM,SimBindProfiles,simpleaffy,sizepower,SMAP,SNAGEE,snapCGH,snm,snpStats,SpeCond,SPIA,spikeLI,spkTools,spotSegmentation,sRAP,ssize,SSPA,STAN,Starr,stepNorm,stepwiseCM,sva,TDARACNE,TEQC,tigre,tilingArray,timecourse,ToPASeq,topGO,tRanslatome,TransView,trigger,trio,tspair,TurboNorm,twilight,vsn,wateRmelon,waveTiling,webbioc,XDE,xps,yaqcaffy", "id": "Microarray" }, "children": [ { "data": "ChipOnChip (1)", "attr": { "packageList": "puma", "id": "ChipOnChip" }, "children": [ ] }, { "childnum": 0, "data": "GenotypingArray", "children": [ ] }, { "data": "MethylationArray (7)", "attr": { "packageList": "ChAMP,DMRcate,MBAmethyl,MethylAid,MethylMix,missMethyl,TurboNorm", "id": "MethylationArray" }, "children": [ ] }, { "childnum": 0, "data": "MicroRNAArray", "children": [ ] }, { "data": "mRNAMicroarray (3)", "attr": { "packageList": "erccdashboard,limma,puma", "id": "mRNAMicroarray" }, "children": [ ] }, { "data": "MultiChannel (3)", "attr": { "packageList": "aroma.light,ELBOW,snm", "id": "MultiChannel" }, "children": [ ] }, { "data": "OneChannel (68)", "attr": { "packageList": "ABarray,affy,affycomp,AffyCompatible,affycoretools,AffyExpress,affyILM,affylmGUI,affypdnn,affyPLM,affyQCReport,AffyRNADegradation,AgiMicroRna,altcdfenvs,annaffy,annmap,aroma.light,ArrayExpress,arrayQualityMetrics,ArrayTools,beadarray,BrainStars,bridge,CAFE,clippda,codelink,copa,DMRcate,ELBOW,ExiMiR,gaga,gage,gcrma,GeneRegionScan,GEOquery,GlobalAncova,globaltest,Harshlight,iChip,lapmix,limma,lmdme,lumi,LVSmiRNA,makecdfenv,mvGST,oligo,oneChannelGUI,PAA,PADOG,plw,PROMISE,puma,pvac,RefPlus,RLMM,SAGx,SCAN.UPC,simpleaffy,SNAGEE,snm,Starr,tilingArray,TurboNorm,vsn,webbioc,xps,yaqcaffy", "id": "OneChannel" }, "children": [ ] }, { "data": "ProprietaryPlatforms (2)", "attr": { "packageList": "altcdfenvs,limma", "id": "ProprietaryPlatforms" }, "children": [ ] }, { "childnum": 0, "data": "ReversePhaseProteinArray", "children": [ ] }, { "childnum": 0, "data": "TissueMicroarray", "children": [ ] }, { "data": "TwoChannel (53)", "attr": { "packageList": "aroma.light,ArrayExpress,arrayQuality,arrayQualityMetrics,ARRmNormalization,asmn,beadarraySNP,bridge,CALIB,ChAMP,convert,copa,daMA,DMRcate,dyebias,ELBOW,ExiMiR,gage,genArise,GEOquery,HELP,limma,limmaGUI,lmdme,lumi,maigesPack,MANOR,marray,MethylAid,methylumi,minfi,MmPalateMiRNA,nnNorm,nudge,oligo,OLIN,OLINgui,PADOG,plw,puma,rama,Ringo,SCAN.UPC,shinyMethyl,SMAP,SNAGEE,snapCGH,snm,spotSegmentation,stepNorm,TurboNorm,vsn,wateRmelon", "id": "TwoChannel" }, "children": [ ] } ] }, { "data": "MicrotitrePlateAssay (13)", "attr": { "packageList": "bioassayR,cellGrowth,ChemmineR,ddCt,fmcsR,HTqPCR,NormqPCR,Rchemcpp,ReadqPCR,SLqPCR,splots,staRank,unifiedWMWqPCR", "id": "MicrotitrePlateAssay" }, "children": [ ] }, { "data": "qPCR (9)", "attr": { "packageList": "ddCt,DECIPHER,EasyqpcR,HTqPCR,nondetects,NormqPCR,ReadqPCR,SLqPCR,unifiedWMWqPCR", "id": "qPCR" }, "children": [ ] }, { "data": "SAGE (9)", "attr": { "packageList": "BADER,baySeq,DESeq,DESeq2,edgeR,GEOquery,MiRaGE,rnaSeqMap,sagenhaft", "id": "SAGE" }, "children": [ ] }, { "data": "Sequencing (212)", "attr": { "packageList": "ALDEx2,AllelicImbalance,ampliQueso,AnnotationDbi,anota,ArrayExpressHTS,BADER,BaseSpaceR,baySeq,biomvRCNS,Biostrings,birta,BiSeq,BitSeq,CAGEr,casper,CexoR,ChIPQC,chipseq,cleanUpdTSeq,Clomial,clonotypeR,clstutils,cn.mops,CNAnorm,CNVrd2,compEpiTools,CorMut,CoverageView,csaw,CSSP,cummeRbund,DBChIP,DECIPHER,deepSNV,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEXSeq,dexus,DiffBind,DirichletMultinomial,DSS,EBSeq,EBSeqHMM,EDASeq,EDDA,edgeR,ELBOW,exomeCopy,exomePeak,facopy,focalCall,FourCSeq,gage,gaucho,GeneMeta,GeneNetworkBuilder,geneRxCluster,GenomicAlignments,GenomicFeatures,GenomicFiles,GenomicRanges,GenomicTuples,girafe,GOexpress,goseq,GOTHiC,groHMM,hapFabia,hiReadsProcessor,HiTC,HMMcopy,htSeqTools,HTSFilter,intansv,interactiveDisplay,interactiveDisplayBase,iSeq,jmosaics,manta,MBASED,mcaGUI,MEDIPS,metaSeq,methylMnM,methylPipe,MethylSeekR,MiRaGE,miRNAtap,mmnet,monocle,mosaics,NarrowPeaks,NGScopy,NOISeq,nucleR,oneChannelGUI,OTUbase,pathview,phyloseq,PICS,PING,polyester,Polyfit,prebs,QDNAseq,qrqc,quantro,QuasR,r3Cseq,R453Plus1Toolbox,Rariant,Rbowtie,Rcade,REDseq,regionReport,ReQON,rGADEM,riboSeqR,RIPSeeker,rnaSeqMap,roar,Rolexa,Rqc,rRDP,Rsamtools,rSFFreader,Rsubread,RSVSim,sangerseqR,savR,segmentSeq,SeqArray,seqbias,seqCNA,SeqGSEA,seqplots,seqTools,SeqVarTools,ShortRead,SomatiCA,SomaticSignatures,spliceR,SplicingGraphs,splots,SRAdb,ssviz,STAN,Sushi,sva,systemPipeR,TCC,TEQC,TitanCNA,tracktables,tRanslatome,TransView,triform,TSSi,tweeDEseq,VariantAnnotation,VariantFiltering,VariantTools,wavClusteR", "id": "Sequencing" }, "children": [ { "data": "ChIPSeq (40)", "attr": { "packageList": "ALDEx2,BayesPeak,ChIPpeakAnno,ChIPQC,ChIPseeker,chipseq,ChIPseqR,ChIPsim,ChIPXpress,cobindR,CoverageView,CSAR,csaw,CSSP,DBChIP,DESeq,DESeq2,DiffBind,DSS,EDDA,edgeR,epigenomix,iASeq,iSeq,jmosaics,MEDIPS,metagene,MMDiff,MotIV,NarrowPeaks,nucleR,PICS,QuasR,Rcade,rGADEM,Rsubread,seqplots,systemPipeR,TransView,triform", "id": "ChIPSeq" }, "children": [ ] }, { "childnum": 0, "data": "DenovoGenome", "children": [ ] }, { "childnum": 0, "data": "DenovoTranscriptome", "children": [ ] }, { "data": "DNASeq (6)", "attr": { "packageList": "ALDEx2,Clomial,CNAnorm,NGScopy,QDNAseq,TitanCNA", "id": "DNASeq" }, "children": [ ] }, { "data": "ExomeSeq (3)", "attr": { "packageList": "Clomial,NGScopy,TitanCNA", "id": "ExomeSeq" }, "children": [ ] }, { "data": "MethylSeq (10)", "attr": { "packageList": "BEAT,BiSeq,COHCAP,methylPipe,MethylSeekR,MPFE,QuasR,Repitools,systemPipeR,TransView", "id": "MethylSeq" }, "children": [ ] }, { "childnum": 0, "data": "MicrobialStrain", "children": [ ] }, { "data": "Microbiome (3)", "attr": { "packageList": "mmnet,phyloseq,rRDP", "id": "Microbiome" }, "children": [ ] }, { "data": "miRNA (4)", "attr": { "packageList": "miRNApath,miRNAtap,Roleswitch,TargetScore", "id": "miRNA" }, "children": [ ] }, { "data": "RIPSeq (1)", "attr": { "packageList": "RIPSeeker", "id": "RIPSeq" }, "children": [ ] }, { "data": "RNASeq (76)", "attr": { "packageList": "ALDEx2,ampliQueso,ArrayExpressHTS,BADER,ballgown,BitSeq,casper,compcodeR,CoverageView,cqn,cummeRbund,DEGreport,DEGseq,derfinder,derfinderHelper,derfinderPlot,DESeq,DESeq2,DEXSeq,dexus,DSS,easyRNASeq,EBSeq,EBSeqHMM,EDASeq,EDDA,edgeR,ELBOW,erccdashboard,flipflop,gage,geecc,GenomicAlignments,GOexpress,goseq,HDTD,HTSFilter,iASeq,limma,manta,metaSeq,metaseqR,MiRaGE,monocle,mvGST,NOISeq,oneChannelGUI,pathview,Polyfit,prebs,QuasR,qusage,regionReport,ReportingTools,rnaSeqMap,RNASeqPower,Rsubread,RUVSeq,sapFinder,SCAN.UPC,SeqGSEA,seqplots,SGSeq,SigFuge,spliceSites,SplicingGraphs,sSeq,SSPA,ssviz,sva,systemPipeR,TCC,ToPASeq,TransView,TSSi,tweeDEseq", "id": "RNASeq" }, "children": [ ] }, { "childnum": 0, "data": "SangerSeq", "children": [ ] }, { "childnum": 0, "data": "SmallRNA", "children": [ ] }, { "data": "TargetedResequencing (2)", "attr": { "packageList": "Clomial,NGScopy", "id": "TargetedResequencing" }, "children": [ ] }, { "data": "WholeGenome (3)", "attr": { "packageList": "CNAnorm,NGScopy,TitanCNA", "id": "WholeGenome" }, "children": [ ] } ] } ] }, { "data": "WorkflowStep (476)", "attr": { "packageList": "geecc,metaseqR,nondetects", "id": "WorkflowStep" }, "children": [ { "data": "Alignment (8)", "attr": { "packageList": "DECIPHER,GenomicAlignments,gmapR,Rbowtie,Rsamtools,Rsubread,segmentSeq,systemPipeR", "id": "Alignment" }, "children": [ ] }, { "data": "Annotation (67)", "attr": { "packageList": "AffyExpress,altcdfenvs,annaffy,annmap,annotate,AnnotationDbi,AnnotationForge,AnnotationHub,annotationTools,ArrayTools,biomaRt,BridgeDbR,BSgenome,Category,categoryCompare,ChIPpeakAnno,ChIPseeker,csaw,DASiR,DAVIDQuery,DMRforPairs,domainsignatures,DOSE,ecolitk,ensemblVEP,ENVISIONQuery,FGNet,FunciSNP,gaggle,gCMAP,GenomeInfoDb,genomes,GenomicFeatures,GenomicRanges,GOexpress,GOstats,hiAnnotator,iBBiG,IdMappingAnalysis,IdMappingRetrieval,intansv,KEGGREST,matchBox,MeSHDbi,meshr,miRNApath,mygene,occugene,OmicCircos,OrganismDbi,PAnnBuilder,pdInfoBuilder,RBioinf,ReactomePA,rfPred,Risa,RNAither,rnaSeqMap,rols,rtracklayer,SemDist,simpleaffy,SplicingGraphs,UniProt.ws,VariantAnnotation,VariantFiltering,xmapbridge", "id": "Annotation" }, "children": [ ] }, { "data": "BatchEffect (5)", "attr": { "packageList": "edgeR,erccdashboard,limma,pvca,sva", "id": "BatchEffect" }, "children": [ ] }, { "data": "ExperimentalDesign (2)", "attr": { "packageList": "EDDA,OSAT", "id": "ExperimentalDesign" }, "children": [ ] }, { "childnum": 0, "data": "GenomeBrowsers", "children": [ ] }, { "data": "MultipleComparison (75)", "attr": { "packageList": "affylmGUI,baySeq,BGmix,bumphunter,categoryCompare,ChIPseeker,clippda,Clomial,clusterProfiler,cnvGSA,cobindR,CompGO,csaw,cummeRbund,dks,DMRcate,DOSE,EBSeq,EBSeqHMM,edgeR,erccdashboard,fabia,fdrame,flowMap,gaga,gage,GeneOverlap,GEWIST,GOexpress,GOstats,HTqPCR,HTSanalyzeR,IdMappingAnalysis,IdMappingRetrieval,LBE,limma,limmaGUI,made4,matchBox,metagene,MineICA,MMDiff,MmPalateMiRNA,monocle,Mulcom,MultiMed,multtest,OCplus,omicade4,oneChannelGUI,OrderedList,parody,PathNet,phenoTest,phyloseq,PROMISE,prot2D,quantro,qvalue,rain,RBioinf,ReactomePA,SAGx,segmentSeq,siggenes,sigPathway,snm,SpeCond,ssviz,staRank,sva,tRanslatome,TransView,twilight,unifiedWMWqPCR", "id": "MultipleComparison" }, "children": [ ] }, { "data": "Normalization (15)", "attr": { "packageList": "ACME,blima,ChAMP,CNAnorm,csaw,EDDA,edgeR,limma,metaseqR,missMethyl,quantro,Rnits,RUVnormalize,sva,TurboNorm", "id": "Normalization" }, "children": [ ] }, { "data": "Pathways (69)", "attr": { "packageList": "annaffy,annotate,ASSIGN,Category,categoryCompare,clusterProfiler,DART,domainsignatures,EnrichmentBrowser,fastLiquidAssociation,FGNet,gage,gCMAP,GlobalAncova,globaltest,GOexpress,GOFunction,GOSemSim,GOstats,graphite,GSReg,GSVA,joda,KEGGgraph,keggorthology,KEGGprofile,KEGGREST,LiquidAssociation,MethylMix,mgsa,miRNApath,mmnet,MmPalateMiRNA,mvGST,NCIgraph,nem,NetPathMiner,npGSEA,occugene,PathNet,pathRender,pathview,paxtoolsr,piano,qpgraph,ReactomePA,rsbml,safe,SBMLR,sigaR,ToPASeq", "id": "Pathways" }, "children": [ { "data": "GO (33)", "attr": { "packageList": "annaffy,annotate,Category,categoryCompare,clusterProfiler,CompGO,FGNet,gage,geecc,globaltest,GOexpress,GOFunction,goProfiles,GOSemSim,goseq,GOSim,GOstats,GOsummaries,goTools,interactiveDisplay,interactiveDisplayBase,mgsa,MmPalateMiRNA,mvGST,pcaGoPromoter,RamiGO,Rcpi,ReportingTools,RNAither,rols,SemDist,sRAP,tRanslatome", "id": "GO" }, "children": [ ] } ] }, { "data": "Preprocessing (128)", "attr": { "packageList": "ABarray,affy,affycomp,AffyExpress,affyILM,affylmGUI,affyPara,affypdnn,affyPLM,AffyRNADegradation,AffyTiling,AgiMicroRna,altcdfenvs,aroma.light,ArrayTools,ARRmNormalization,asmn,ballgown,beadarray,beadarraySNP,biovizBase,blima,BUS,CAGEr,CALIB,cellHTS2,CGHcall,CGHnormaliter,clippda,codelink,CopyNumber450k,cqn,crlmm,DEGseq,DupChecker,dyebias,easyRNASeq,EDASeq,ExiMiR,farms,flowWorkspace,focalCall,FourCSeq,frma,frmaTools,gcrma,genArise,GOTHiC,gprege,Harshlight,HELP,hiReadsProcessor,HMMcopy,HTqPCR,HTSFilter,iBMQ,imageHTS,limma,limmaGUI,LMGene,lumi,LVSmiRNA,maCorrPlot,maigesPack,makecdfenv,MANOR,marray,MBCB,MEDIPS,metaseqR,methylumi,Mfuzz,MiChip,minfi,mitoODE,MmPalateMiRNA,multiscan,nnNorm,nondetects,NTW,oligo,OLIN,OLINgui,oneChannelGUI,openCyto,PECA,pepStat,piano,prebs,puma,QDNAseq,qpcrNorm,qrqc,quantro,QuasR,r3Cseq,rama,RBioinf,REDseq,RefPlus,ReQON,Ringo,rMAT,RNAinteract,RNAither,Rolexa,RPA,Rsubread,RUVSeq,SAGx,SCAN.UPC,scsR,shinyMethyl,simpleaffy,snapCGH,snm,spotSegmentation,sRAP,Starr,stepNorm,sva,TargetSearch,tilingArray,TSSi,TurboNorm,vsn,wateRmelon,xps", "id": "Preprocessing" }, "children": [ ] }, { "data": "QualityControl (95)", "attr": { "packageList": "AffyExpress,affylmGUI,affyPLM,affyQCReport,AffyRNADegradation,altcdfenvs,arrayMvout,arrayQuality,arrayQualityMetrics,ArrayTools,asmn,Basic4Cseq,beadarray,ChIPQC,chipseq,clstutils,CopyNumber450k,CSSP,cummeRbund,DECIPHER,dexus,dks,DMRcate,dyebias,EDASeq,edgeR,erccdashboard,farms,ffpe,flowClean,flowPhyto,GWASTools,Harshlight,HELP,HTqPCR,htSeqTools,ibh,interactiveDisplay,interactiveDisplayBase,isobar,limma,limmaGUI,lumi,MANOR,manta,massiR,mdqc,MEDIPS,metaseqR,MethylAid,methylumi,minfi,MmPalateMiRNA,monocle,MSnbase,OLIN,OLINgui,oneChannelGUI,OSAT,piano,pRoloc,proteoQC,pvac,qcmetrics,QDNAseq,qrqc,R453Plus1Toolbox,rama,RBioinf,ReQON,Ringo,RNAinteract,RNAither,Rolexa,RPA,Rqc,Rsamtools,Rsubread,segmentSeq,seqTools,shinyMethyl,ShortRead,simpleaffy,SNAGEE,snm,spikeLI,spotSegmentation,sRAP,Starr,systemPipeR,TEQC,tRanslatome,unifiedWMWqPCR,wateRmelon,yaqcaffy", "id": "QualityControl" }, "children": [ ] }, { "data": "ReportWriting (25)", "attr": { "packageList": "affycoretools,AffyExpress,ampliQueso,annaffy,annmap,arrayQualityMetrics,ArrayTools,ChIPQC,DEGreport,DMRforPairs,DynDoc,EnrichmentBrowser,Harshlight,metaseqR,MmPalateMiRNA,proteoQC,qcmetrics,R453Plus1Toolbox,rnaSeqMap,sapFinder,simpleaffy,SpeCond,tracktables,xmapbridge,yaqcaffy", "id": "ReportWriting" }, "children": [ ] }, { "data": "Visualization (218)", "attr": { "packageList": "AffyExpress,ampliQueso,annmap,aroma.light,arrayQuality,ArrayTools,Basic4Cseq,BiGGR,bioassayR,biocGraph,BioMVCClass,biomvRCNS,biosvd,biovizBase,CAGEr,cancerclass,cellGrowth,cellHTS,cellHTS2,CGHcall,CGHregions,ChemmineR,ChIPseeker,chroGPS,ChromHeatMap,clstutils,clusterProfiler,CNEr,compEpiTools,CompGO,copa,copynumber,CoRegNet,CoverageView,ctc,cummeRbund,dagLogo,DECIPHER,DEGreport,deltaGseg,derfinderPlot,DMRforPairs,DOSE,EBImage,ecolitk,eisa,EnrichmentBrowser,epivizr,explorase,ExpressionView,fabia,facopy,FGNet,flowcatchR,flowCHIC,flowClust,flowCyBar,flowFP,flowPhyto,flowPlots,flowViz,fmcsR,focalCall,gaggle,gCMAPWeb,GeneAnswers,genefu,GeneOverlap,geneplotter,GeneRegionScan,GenomeGraphs,GenoView,ggbio,GOexpress,GOsummaries,goTools,GSCA,Gviz,hapFabia,Heatplus,HELP,HilbertVis,HilbertVisGUI,HMMcopy,HTqPCR,hyperdraw,IdeoViz,idiogram,imageHTS,interactiveDisplay,interactiveDisplayBase,KCsmart,KEGGgraph,keggorthology,lmdme,macat,maCorrPlot,manta,MassArray,matchBox,mcaGUI,MEDIPS,MergeMaid,metagenomeSeq,methyAnalysis,MethylAid,Mfuzz,MineICA,monocle,motifStack,MSGFgui,MVCClass,NarrowPeaks,netbiov,NetSAM,NOISeq,NuPoP,OLIN,OLINgui,OmicCircos,oposSOM,OSAT,PANR,pathRender,pathview,Pbase,pcaGoPromoter,piano,PICS,PING,prada,pRolocGUI,proteoQC,Pviz,qrqc,quantsmooth,R453Plus1Toolbox,RamiGO,Rariant,RCASPAR,Rchemcpp,RCytoscape,RDAVIDWebService,RDRToolbox,ReactomePA,reb,RedeR,regionReport,ReportingTools,Rgraphviz,riboSeqR,RmiR,RNAinteract,RNAither,rnaSeqMap,RTCA,rtracklayer,sangerseqR,sapFinder,seqplots,SigFuge,SIM,simpleaffy,SNPchip,SomaticSignatures,spade,spliceR,SplicingGraphs,splots,SQUADD,sRAP,ssviz,supraHex,survcomp,Sushi,SwimR,tilingArray,ToPASeq,topGO,trackViewer,TransView,TSCAN,unifiedWMWqPCR,xmapbridge", "id": "Visualization" }, "children": [ { "data": "Network (44)", "attr": { "packageList": "BiGGR,BioNet,BiRewire,CNORfuzzy,CoRegNet,COSNet,DEGraph,DriverNet,EnrichmentBrowser,FEM,FGNet,GOSemSim,GOSim,GraphAlignment,GraphAT,graphite,GRENITS,interactiveDisplay,interactiveDisplayBase,LiquidAssociation,lpNet,MethylMix,minet,netbiov,NetPathMiner,netresponse,NetSAM,networkBMA,pathifier,paxtoolsr,PCpheno,ppiStats,RBGL,RedeR,rsbml,rTRM,rTRMui,SANTA,SBMLR,SLGI,SPEM,SQUADD,STRINGdb,vtpnet", "id": "Network" }, "children": [ ] } ] } ] } ] }, { "data": "AnnotationData (895)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,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.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,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.Celegans.UCSC.ce10,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.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,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.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.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.Mfuro.UCSC.musFur1,BSgenome.Mmulatta.UCSC.rheMac2,BSgenome.Mmulatta.UCSC.rheMac2.masked,BSgenome.Mmulatta.UCSC.rheMac3,BSgenome.Mmulatta.UCSC.rheMac3.masked,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.Ptroglodytes.UCSC.panTro2,BSgenome.Ptroglodytes.UCSC.panTro2.masked,BSgenome.Ptroglodytes.UCSC.panTro3,BSgenome.Ptroglodytes.UCSC.panTro3.masked,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tgondii.ToxoDB.7.0,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,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,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,FDb.FANTOM4.promoters.hg19,FDb.InfiniumMethylation.hg18,FDb.InfiniumMethylation.hg19,FDb.UCSC.snp135common.hg19,FDb.UCSC.snp137common.hg19,FDb.UCSC.tRNAs,fly.db0,gahgu133a.db,gahgu133acdf,gahgu133aprobe,gahgu133b.db,gahgu133bcdf,gahgu133bprobe,gahgu133plus2.db,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2.db,gahgu95av2cdf,gahgu95av2probe,gahgu95b.db,gahgu95bcdf,gahgu95bprobe,gahgu95c.db,gahgu95ccdf,gahgu95cprobe,gahgu95d.db,gahgu95dcdf,gahgu95dprobe,gahgu95e.db,gahgu95ecdf,gahgu95eprobe,genomewidesnp5Crlmm,genomewidesnp6Crlmm,GGHumanMethCancerPanelv1.db,GO.db,gp53cdf,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,hs25kresogen.db,Hs6UG171.db,HsAgilentDesign026652.db,Hspec,hspeccdf,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,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450k.db,IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylation450kprobe,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,illuminaMousev1.db,illuminaMousev1p1.db,illuminaMousev2.db,illuminaRatv1.db,indac.db,JazaeriMetaData.db,KEGG.db,LAPOINTE.db,lumiHumanAll.db,lumiHumanIDMapping,lumiMouseAll.db,lumiMouseIDMapping,lumiRatAll.db,lumiRatIDMapping,m10kcod.db,m20kcod.db,MafDb.ALL.wgs.phase1.release.v3.20101123,MafDb.ESP6500SI.V2.SSA137.dbSNP138,maizecdf,maizeprobe,malaria.db0,medicagocdf,medicagoprobe,MeSH.AOR.db,MeSH.db,MeSH.PCR.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,mirbase.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,mta10stprobeset.db,mta10sttranscriptcluster.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.Hs.ipi.db,org.MeSH.Aca.db,org.MeSH.Aga.PEST.db,org.MeSH.Ame.db,org.MeSH.Aml.db,org.MeSH.Ana.db,org.MeSH.Ani.FGSC.db,org.MeSH.Ath.db,org.MeSH.Atu.K84.db,org.MeSH.Bfl.db,org.MeSH.Bsu.168.db,org.MeSH.Bsu.Bsn5.db,org.MeSH.Bsu.RONN1.db,org.MeSH.Bsu.TUB10.db,org.MeSH.Bsu.W23.db,org.MeSH.Bta.db,org.MeSH.Cal.SC5314.db,org.MeSH.Cbr.db,org.MeSH.Cel.db,org.MeSH.Cfa.db,org.MeSH.Cin.db,org.MeSH.Cja.db,org.MeSH.Cpo.db,org.MeSH.Cre.db,org.MeSH.Dan.db,org.MeSH.Dda.3937.db,org.MeSH.Ddi.AX4.db,org.MeSH.Der.db,org.MeSH.Dgr.db,org.MeSH.Dme.db,org.MeSH.Dmo.db,org.MeSH.Dpe.db,org.MeSH.Dre.db,org.MeSH.Dse.db,org.MeSH.Dsi.db,org.MeSH.Dvi.db,org.MeSH.Dya.db,org.MeSH.Eco.536.db,org.MeSH.Eco.55989.db,org.MeSH.Eco.APEC01.db,org.MeSH.Eco.B.REL606.db,org.MeSH.Eco.BW2952.db,org.MeSH.Eco.CFT073.db,org.MeSH.Eco.E24377A.db,org.MeSH.Eco.ED1a.db,org.MeSH.Eco.HS.db,org.MeSH.Eco.IAI1.db,org.MeSH.Eco.IAI39.db,org.MeSH.Eco.K12.DH10B.db,org.MeSH.Eco.K12.MG1655.db,org.MeSH.Eco.KO11FL.db,org.MeSH.Eco.O103.H2.12009.db,org.MeSH.Eco.O111.H.11128.db,org.MeSH.Eco.O127.H6.E2348.69.db,org.MeSH.Eco.O157.H7.EC4115.db,org.MeSH.Eco.O157.H7.EDL933.db,org.MeSH.Eco.O157.H7.Sakai.db,org.MeSH.Eco.O157.H7.TW14359.db,org.MeSH.Eco.O26.H11.11368.db,org.MeSH.Eco.O26.H7.CB9615.db,org.MeSH.Eco.S88.db,org.MeSH.Eco.SE11.db,org.MeSH.Eco.SMS35.db,org.MeSH.Eco.UMN026.db,org.MeSH.Eco.UTI89.db,org.MeSH.Eqc.db,org.MeSH.Gga.db,org.MeSH.Gma.db,org.MeSH.Hsa.db,org.MeSH.Laf.db,org.MeSH.Lma.db,org.MeSH.Mdo.db,org.MeSH.Mes.db,org.MeSH.Mga.db,org.MeSH.Miy.db,org.MeSH.Mml.db,org.MeSH.Mmu.db,org.MeSH.Mtr.db,org.MeSH.Nle.db,org.MeSH.Oan.db,org.MeSH.Ocu.db,org.MeSH.Oni.db,org.MeSH.Osa.db,org.MeSH.Pab.db,org.MeSH.Pae.LESB58.db,org.MeSH.Pae.PA14.db,org.MeSH.Pae.PA7.db,org.MeSH.Pae.PAO1.db,org.MeSH.Pfa.3D7.db,org.MeSH.Pto.db,org.MeSH.Ptr.db,org.MeSH.Rno.db,org.MeSH.Sau.COL.db,org.MeSH.Sau.ED98.db,org.MeSH.Sau.M013.db,org.MeSH.Sau.MRSA252.db,org.MeSH.Sau.MSHR1132.db,org.MeSH.Sau.MSSA476.db,org.MeSH.Sau.Mu3.db,org.MeSH.Sau.Mu50.db,org.MeSH.Sau.MW2.db,org.MeSH.Sau.N315.db,org.MeSH.Sau.Newman.db,org.MeSH.Sau.RF122.db,org.MeSH.Sau.USA300FPR3757.db,org.MeSH.Sau.USA300TCH1516.db,org.MeSH.Sau.VC40.db,org.MeSH.Sce.S288c.db,org.MeSH.Sco.A32.db,org.MeSH.Sil.db,org.MeSH.Spo.972h.db,org.MeSH.Spu.db,org.MeSH.Ssc.db,org.MeSH.Syn.db,org.MeSH.Tbr.9274.db,org.MeSH.Tgo.ME49.db,org.MeSH.Tgu.db,org.MeSH.Vvi.db,org.MeSH.Xla.db,org.MeSH.Xtr.db,org.MeSH.Zma.db,org.Mm.eg.db,org.Mmu.eg.db,org.Pf.plasmo.db,org.Pt.eg.db,org.Rn.eg.db,org.Sc.sgd.db,org.Sco.eg.db,org.Ss.eg.db,org.Tgondii.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.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.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.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,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,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,ricecdf,riceprobe,RmiR.Hs.miRNA,RmiR.hsa,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,Roberts2005Annotation.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,saureuscdf,saureusprobe,SHDZ.db,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,SNPlocs.Hsapiens.dbSNP.20090506,SNPlocs.Hsapiens.dbSNP.20100427,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20110815,SNPlocs.Hsapiens.dbSNP.20111119,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,soybeancdf,soybeanprobe,sugarcanecdf,sugarcaneprobe,targetscan.Hs.eg.db,targetscan.Mm.eg.db,test1cdf,test2cdf,test3cdf,test3probe,tomatocdf,tomatoprobe,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Celegans.UCSC.ce6.ensGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,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.Mmusculus.UCSC.mm10.ensGene,TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm9.knownGene,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene,TxDb.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,wheatcdf,wheatprobe,worm.db0,xenopus.db0,xenopuslaeviscdf,xenopuslaevisprobe,xlaevis.db,xlaevis2cdf,xlaevis2probe,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 (374)", "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,cottoncdf,cottonprobe,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliprobe,gahgu133acdf,gahgu133aprobe,gahgu133bcdf,gahgu133bprobe,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2cdf,gahgu95av2probe,gahgu95bcdf,gahgu95bprobe,gahgu95ccdf,gahgu95cprobe,gahgu95dcdf,gahgu95dprobe,gahgu95ecdf,gahgu95eprobe,GGHumanMethCancerPanelv1.db,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,hgug4100a.db,hgug4101a.db,hgug4110b.db,hgug4111a.db,hgug4112a.db,hguqiagenv3.db,hivprtplus2cdf,hs25kresogen.db,HsAgilentDesign026652.db,Hspec,hspeccdf,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,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450k.db,IlluminaHumanMethylation450kmanifest,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,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,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,mta10stprobeset.db,mta10sttranscriptcluster.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,rat2302probe,rattoxfxcdf,rattoxfxprobe,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rgug4105a.db,rgug4130a.db,rgug4131a.db,rhesuscdf,rhesusprobe,ricecdf,riceprobe,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,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": "ChipManufacturer" }, "children": [ { "data": "AffymetrixChip (336)", "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,cottoncdf,cottonprobe,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliprobe,gahgu133acdf,gahgu133aprobe,gahgu133bcdf,gahgu133bprobe,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2cdf,gahgu95av2probe,gahgu95bcdf,gahgu95bprobe,gahgu95ccdf,gahgu95cprobe,gahgu95dcdf,gahgu95dprobe,gahgu95ecdf,gahgu95eprobe,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,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,mta10stprobeset.db,mta10sttranscriptcluster.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,rat2302probe,rattoxfxcdf,rattoxfxprobe,rgu34a.db,rgu34acdf,rgu34aprobe,rgu34b.db,rgu34bcdf,rgu34bprobe,rgu34c.db,rgu34ccdf,rgu34cprobe,rhesuscdf,rhesusprobe,ricecdf,riceprobe,rnu34.db,rnu34cdf,rnu34probe,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": [ ] }, { "childnum": 0, "data": "GEChip", "children": [ ] }, { "data": "IlluminaChip (19)", "attr": { "packageList": "GGHumanMethCancerPanelv1.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450k.db,IlluminaHumanMethylation450kmanifest,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 (195)", "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,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 (3)", "attr": { "packageList": "rat2302.db,rat2302cdf,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": [ ] }, { "data": "CustomCDF (16)", "attr": { "packageList": "gahgu133acdf,gahgu133aprobe,gahgu133bcdf,gahgu133bprobe,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2cdf,gahgu95av2probe,gahgu95bcdf,gahgu95bprobe,gahgu95ccdf,gahgu95cprobe,gahgu95dcdf,gahgu95dprobe,gahgu95ecdf,gahgu95eprobe", "id": "CustomCDF" }, "children": [ { "data": "GACustomCDF (16)", "attr": { "packageList": "gahgu133acdf,gahgu133aprobe,gahgu133bcdf,gahgu133bprobe,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2cdf,gahgu95av2probe,gahgu95bcdf,gahgu95bprobe,gahgu95ccdf,gahgu95cprobe,gahgu95dcdf,gahgu95dprobe,gahgu95ecdf,gahgu95eprobe", "id": "GACustomCDF" }, "children": [ ] }, { "childnum": 0, "data": "MBNICustomCDF", "children": [ ] } ] }, { "data": "CustomDBSchema (11)", "attr": { "packageList": "ChemmineDrugs,RmiR.Hs.miRNA,RmiR.hsa", "id": "CustomDBSchema" }, "children": [ { "data": "GeneCardsCustomSchema (8)", "attr": { "packageList": "gahgu133a.db,gahgu133b.db,gahgu133plus2.db,gahgu95av2.db,gahgu95b.db,gahgu95c.db,gahgu95d.db,gahgu95e.db", "id": "GeneCardsCustomSchema" }, "children": [ ] } ] }, { "data": "FunctionalAnnotation (13)", "attr": { "packageList": "DO.db,GO.db,humanCHRLOC,KEGG.db,MeSH.AOR.db,MeSH.db,MeSH.PCR.db,mirbase.db,mouseCHRLOC,ratCHRLOC,reactome.db,targetscan.Hs.eg.db,targetscan.Mm.eg.db", "id": "FunctionalAnnotation" }, "children": [ ] }, { "data": "Organism (532)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,anopheles.db0,arabidopsis.db0,ath1121501.db,ath1121501cdf,ath1121501probe,barley1cdf,barley1probe,bovine.db,bovine.db0,bovinecdf,bovineprobe,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,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.Celegans.UCSC.ce10,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.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,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.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.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.Mmulatta.UCSC.rheMac2,BSgenome.Mmulatta.UCSC.rheMac2.masked,BSgenome.Mmulatta.UCSC.rheMac3,BSgenome.Mmulatta.UCSC.rheMac3.masked,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.Ptroglodytes.UCSC.panTro2,BSgenome.Ptroglodytes.UCSC.panTro2.masked,BSgenome.Ptroglodytes.UCSC.panTro3,BSgenome.Ptroglodytes.UCSC.panTro3.masked,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,bsubtiliscdf,bsubtilisprobe,canine.db,canine.db0,canine2.db,canine2cdf,canine2probe,caninecdf,canineprobe,celegans.db,celeganscdf,celegansprobe,chicken.db,chicken.db0,chickencdf,chickenprobe,chimp.db0,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliK12.db0,ecoliprobe,ecoliSakai.db0,FDb.FANTOM4.promoters.hg19,FDb.InfiniumMethylation.hg18,FDb.InfiniumMethylation.hg19,FDb.UCSC.snp135common.hg19,FDb.UCSC.snp137common.hg19,FDb.UCSC.tRNAs,fly.db0,gahgu133aprobe,gahgu133bprobe,gahgu133plus2probe,gahgu95av2probe,gahgu95bprobe,gahgu95cprobe,gahgu95dprobe,gahgu95eprobe,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.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,hs25kresogen.db,Hs6UG171.db,HsAgilentDesign026652.db,Hspec,hspeccdf,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,humanCHRLOC,HuO22.db,hwgcod.db,IlluminaHumanMethylation27k.db,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450k.db,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylation450kprobe,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.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,MafDb.ALL.wgs.phase1.release.v3.20101123,MafDb.ESP6500SI.V2.SSA137.dbSNP138,maizecdf,maizeprobe,malaria.db0,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,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,mm24kresogen.db,MmAgilentDesign026655.db,moe430a.db,moe430acdf,moe430aprobe,moe430b.db,moe430bcdf,moe430bprobe,moex10stprobeset.db,moex10sttranscriptcluster.db,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,mta10stprobeset.db,mta10sttranscriptcluster.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,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.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,PartheenMetaData.db,pedbarrayv10.db,pedbarrayv9.db,phastCons100way.UCSC.hg19,pig.db0,plasmodiumanophelescdf,plasmodiumanophelescdf,plasmodiumanophelesprobe,plasmodiumanophelesprobe,POCRCannotation.db,PolyPhen.Hsapiens.dbSNP131,porcine.db,porcinecdf,porcineprobe,primeviewcdf,primeviewprobe,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,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,rhesuscdf,rhesusprobe,ri16cod.db,RmiR.Hs.miRNA,RmiR.hsa,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,Roberts2005Annotation.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,saureuscdf,saureusprobe,SHDZ.db,SIFT.Hsapiens.dbSNP132,SIFT.Hsapiens.dbSNP137,SNPlocs.Hsapiens.dbSNP.20090506,SNPlocs.Hsapiens.dbSNP.20100427,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20110815,SNPlocs.Hsapiens.dbSNP.20111119,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.GRCh38,sugarcanecdf,sugarcaneprobe,test1cdf,test2cdf,test3cdf,test3probe,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Celegans.UCSC.ce6.ensGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,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.Mmusculus.UCSC.mm10.ensGene,TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm9.knownGene,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene,TxDb.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,worm.db0,xenopus.db0,xlaevis.db,xtropicalisprobe,ye6100subacdf,ye6100subbcdf,ye6100subccdf,ye6100subdcdf,yeast.db0,yeast2.db,yeast2cdf,yeast2probe,ygs98.db,ygs98cdf,ygs98probe,zebrafish.db,zebrafish.db0,zebrafishcdf,zebrafishprobe", "id": "Organism" }, "children": [ { "data": "Anopheles_gambiae (4)", "attr": { "packageList": "anopheles.db0,org.Ag.eg.db,plasmodiumanophelescdf,plasmodiumanophelesprobe", "id": "Anopheles_gambiae" }, "children": [ ] }, { "data": "Apis_mellifera (3)", "attr": { "packageList": "BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked", "id": "Apis_mellifera" }, "children": [ ] }, { "childnum": 0, "data": "Arabidopsis_lyrata", "children": [ ] }, { "data": "Arabidopsis_thaliana (12)", "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", "id": "Arabidopsis_thaliana" }, "children": [ ] }, { "data": "Bacillus_subtilis (2)", "attr": { "packageList": "bsubtiliscdf,bsubtilisprobe", "id": "Bacillus_subtilis" }, "children": [ ] }, { "data": "Bos_taurus (11)", "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,org.Bt.eg.db", "id": "Bos_taurus" }, "children": [ ] }, { "data": "Caenorhabditis_elegans (10)", "attr": { "packageList": "BSgenome.Celegans.UCSC.ce10,BSgenome.Celegans.UCSC.ce2,BSgenome.Celegans.UCSC.ce6,celegans.db,celeganscdf,celegansprobe,hom.Ce.inp.db,org.Ce.eg.db,TxDb.Celegans.UCSC.ce6.ensGene,worm.db0", "id": "Caenorhabditis_elegans" }, "children": [ ] }, { "data": "Canis_familiaris (12)", "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", "id": "Canis_familiaris" }, "children": [ ] }, { "childnum": 0, "data": "Ciona_intestinalis", "children": [ ] }, { "data": "Danio_rerio (12)", "attr": { "packageList": "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,zebrafish.db,zebrafish.db0,zebrafishcdf,zebrafishprobe", "id": "Danio_rerio" }, "children": [ ] }, { "data": "Drosophila_melanogaster (15)", "attr": { "packageList": "BSgenome.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,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", "id": "Drosophila_melanogaster" }, "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 (9)", "attr": { "packageList": "BSgenome.Ggallus.UCSC.galGal3,BSgenome.Ggallus.UCSC.galGal3.masked,BSgenome.Ggallus.UCSC.galGal4,BSgenome.Ggallus.UCSC.galGal4.masked,chicken.db,chicken.db0,chickencdf,chickenprobe,org.Gg.eg.db", "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 (201)", "attr": { "packageList": "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,cyp450cdf,FDb.FANTOM4.promoters.hg19,FDb.InfiniumMethylation.hg18,FDb.InfiniumMethylation.hg19,FDb.UCSC.snp135common.hg19,FDb.UCSC.snp137common.hg19,FDb.UCSC.tRNAs,gahgu133aprobe,gahgu133bprobe,gahgu133plus2probe,gahgu95av2probe,gahgu95bprobe,gahgu95cprobe,gahgu95dprobe,gahgu95eprobe,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,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,IlluminaHumanMethylation27kmanifest,IlluminaHumanMethylation450k.db,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylation450kprobe,illuminaHumanv1.db,illuminaHumanv2.db,illuminaHumanv2BeadID.db,illuminaHumanv3.db,illuminaHumanv4.db,illuminaHumanWGDASLv3.db,illuminaHumanWGDASLv4.db,JazaeriMetaData.db,LAPOINTE.db,lumiHumanAll.db,MafDb.ALL.wgs.phase1.release.v3.20101123,MafDb.ESP6500SI.V2.SSA137.dbSNP138,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,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.20090506,SNPlocs.Hsapiens.dbSNP.20100427,SNPlocs.Hsapiens.dbSNP.20101109,SNPlocs.Hsapiens.dbSNP.20110815,SNPlocs.Hsapiens.dbSNP.20111119,SNPlocs.Hsapiens.dbSNP.20120608,SNPlocs.Hsapiens.dbSNP141.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", "id": "Homo_sapiens" }, "children": [ ] }, { "data": "Hordeum_vulgare (2)", "attr": { "packageList": "barley1cdf,barley1probe", "id": "Hordeum_vulgare" }, "children": [ ] }, { "childnum": 0, "data": "Kluyveromyces_lactis", "children": [ ] }, { "data": "Macaca_mulatta (7)", "attr": { "packageList": "BSgenome.Mmulatta.UCSC.rheMac2,BSgenome.Mmulatta.UCSC.rheMac2.masked,BSgenome.Mmulatta.UCSC.rheMac3,BSgenome.Mmulatta.UCSC.rheMac3.masked,org.Mmu.eg.db,rhesuscdf,rhesusprobe", "id": "Macaca_mulatta" }, "children": [ ] }, { "childnum": 0, "data": "Magnaporthe_grisea", "children": [ ] }, { "childnum": 0, "data": "Medicago_truncatula", "children": [ ] }, { "data": "Mus_musculus (103)", "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,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,mta10stprobeset.db,mta10sttranscriptcluster.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.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_troglodytes (6)", "attr": { "packageList": "BSgenome.Ptroglodytes.UCSC.panTro2,BSgenome.Ptroglodytes.UCSC.panTro2.masked,BSgenome.Ptroglodytes.UCSC.panTro3,BSgenome.Ptroglodytes.UCSC.panTro3.masked,chimp.db0,org.Pt.eg.db", "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 (65)", "attr": { "packageList": "adme16cod.db,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,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,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,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene", "id": "Rattus_norvegicus" }, "children": [ ] }, { "data": "Saccharomyces_cerevisiae (18)", "attr": { "packageList": "BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.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 (7)", "attr": { "packageList": "BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,org.Ss.eg.db,pig.db0,porcine.db,porcinecdf,porcineprobe", "id": "Sus_scrofa" }, "children": [ ] }, { "data": "Taeniopygia_guttata (2)", "attr": { "packageList": "BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked", "id": "Taeniopygia_guttata" }, "children": [ ] }, { "childnum": 0, "data": "Triticum_aestivum", "children": [ ] }, { "data": "Vitis_vinifera (2)", "attr": { "packageList": "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 (524)", "attr": { "packageList": "adme16cod.db,ag.db,agcdf,agprobe,anopheles.db0,arabidopsis.db0,ath1121501.db,ath1121501cdf,ath1121501probe,barley1cdf,barley1probe,bovine.db,bovine.db0,bovinecdf,bovineprobe,BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,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.Celegans.UCSC.ce10,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.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,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.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.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.Mfuro.UCSC.musFur1,BSgenome.Mmulatta.UCSC.rheMac2,BSgenome.Mmulatta.UCSC.rheMac2.masked,BSgenome.Mmulatta.UCSC.rheMac3,BSgenome.Mmulatta.UCSC.rheMac3.masked,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.Ptroglodytes.UCSC.panTro2,BSgenome.Ptroglodytes.UCSC.panTro2.masked,BSgenome.Ptroglodytes.UCSC.panTro3,BSgenome.Ptroglodytes.UCSC.panTro3.masked,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked,bsubtiliscdf,bsubtilisprobe,canine.db,canine.db0,canine2.db,canine2cdf,canine2probe,caninecdf,canineprobe,celegans.db,celeganscdf,celegansprobe,chicken.db,chicken.db0,chickencdf,chickenprobe,chimp.db0,citruscdf,citrusprobe,cottoncdf,cottonprobe,cyp450cdf,drosgenome1.db,drosgenome1cdf,drosgenome1probe,drosophila2.db,drosophila2cdf,drosophila2probe,ecoli2.db,ecoli2cdf,ecoli2probe,ecoliasv2cdf,ecoliasv2probe,ecolicdf,ecoliK12.db0,ecoliprobe,ecoliSakai.db0,FDb.UCSC.tRNAs,fly.db0,gahgu133acdf,gahgu133aprobe,gahgu133bcdf,gahgu133bprobe,gahgu133plus2cdf,gahgu133plus2probe,gahgu95av2cdf,gahgu95av2probe,gahgu95bcdf,gahgu95bprobe,gahgu95ccdf,gahgu95cprobe,gahgu95dcdf,gahgu95dprobe,gahgu95ecdf,gahgu95eprobe,gp53cdf,h10kcod.db,h20kcod.db,hcg110.db,hcg110cdf,hcg110probe,hgfocus.db,hgfocuscdf,hgfocusprobe,hgu133a.db,hgu133a2.db,hgu133a2cdf,hgu133a2probe,hgu133acdf,hgu133aprobe,hgu133atagcdf,hgu133atagprobe,hgu133b.db,hgu133bcdf,hgu133bprobe,hgu133plus2.db,hgu133plus2cdf,hgu133plus2probe,hgu219.db,hgu219cdf,hgu219probe,hgu95a.db,hgu95acdf,hgu95aprobe,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,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,Hs6UG171.db,HsAgilentDesign026652.db,Hspec,hspeccdf,hthgu133a.db,hthgu133acdf,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,huex10stprobeset.db,huex10sttranscriptcluster.db,HuExExonProbesetLocation,hugene10stprobeset.db,hugene10sttranscriptcluster.db,hugene10stv1cdf,hugene10stv1probe,hugene11stprobeset.db,hugene11sttranscriptcluster.db,hugene20stprobeset.db,hugene20sttranscriptcluster.db,hugene21stprobeset.db,hugene21sttranscriptcluster.db,human.db0,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,maizecdf,maizeprobe,malaria.db0,medicagocdf,medicagoprobe,MeSH.AOR.db,MeSH.db,MeSH.PCR.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,mirna102xgaincdf,mirna10cdf,mirna10probe,mirna20cdf,MmAgilentDesign026655.db,moe430a.db,moe430acdf,moe430aprobe,moe430b.db,moe430bcdf,moe430bprobe,moex10stprobeset.db,moex10sttranscriptcluster.db,MoExExonProbesetLocation,mogene10stprobeset.db,mogene10sttranscriptcluster.db,mogene10stv1cdf,mogene10stv1probe,mogene11stprobeset.db,mogene11sttranscriptcluster.db,mogene20stprobeset.db,mogene20sttranscriptcluster.db,mogene21stprobeset.db,mogene21sttranscriptcluster.db,mouse.db0,mouse4302.db,mouse4302cdf,mouse4302probe,mouse430a2.db,mouse430a2cdf,mouse430a2probe,mpedbarray.db,mta10stprobeset.db,mta10sttranscriptcluster.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,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.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,PartheenMetaData.db,pedbarrayv10.db,pedbarrayv9.db,pig.db0,plasmodiumanophelescdf,plasmodiumanophelesprobe,POCRCannotation.db,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,rat2302probe,rattoxfxcdf,rattoxfxprobe,Rattus.norvegicus,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,ricecdf,riceprobe,RnAgilentDesign028282.db,rnu34.db,rnu34cdf,rnu34probe,Roberts2005Annotation.db,rtu34.db,rtu34cdf,rtu34probe,rwgcod.db,saureuscdf,saureusprobe,SHDZ.db,SNPlocs.Hsapiens.dbSNP141.GRCh38,soybeancdf,soybeanprobe,sugarcanecdf,sugarcaneprobe,test1cdf,test2cdf,test3cdf,test3probe,tomatocdf,tomatoprobe,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Celegans.UCSC.ce6.ensGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,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.Mmusculus.UCSC.mm10.ensGene,TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm9.knownGene,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene,TxDb.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,u133aaofav2cdf,u133x3p.db,u133x3pcdf,u133x3pprobe,vitisviniferacdf,vitisviniferaprobe,wheatcdf,wheatprobe,worm.db0,xenopus.db0,xenopuslaeviscdf,xenopuslaevisprobe,xlaevis.db,xlaevis2cdf,xlaevis2probe,xtropicaliscdf,xtropicalisprobe,ye6100subacdf,ye6100subbcdf,ye6100subccdf,ye6100subdcdf,yeast.db0,yeast2.db,yeast2cdf,yeast2probe,ygs98.db,ygs98cdf,ygs98probe,zebrafish.db,zebrafish.db0,zebrafishcdf,zebrafishprobe", "id": "PackageType" }, "children": [ { "data": "BSgenome (69)", "attr": { "packageList": "BSgenome.Amellifera.BeeBase.assembly4,BSgenome.Amellifera.UCSC.apiMel2,BSgenome.Amellifera.UCSC.apiMel2.masked,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.Celegans.UCSC.ce10,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.Dmelanogaster.UCSC.dm2,BSgenome.Dmelanogaster.UCSC.dm2.masked,BSgenome.Dmelanogaster.UCSC.dm3,BSgenome.Dmelanogaster.UCSC.dm3.masked,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.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.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.Mfuro.UCSC.musFur1,BSgenome.Mmulatta.UCSC.rheMac2,BSgenome.Mmulatta.UCSC.rheMac2.masked,BSgenome.Mmulatta.UCSC.rheMac3,BSgenome.Mmulatta.UCSC.rheMac3.masked,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.Ptroglodytes.UCSC.panTro2,BSgenome.Ptroglodytes.UCSC.panTro2.masked,BSgenome.Ptroglodytes.UCSC.panTro3,BSgenome.Ptroglodytes.UCSC.panTro3.masked,BSgenome.Rnorvegicus.UCSC.rn4,BSgenome.Rnorvegicus.UCSC.rn4.masked,BSgenome.Rnorvegicus.UCSC.rn5,BSgenome.Rnorvegicus.UCSC.rn5.masked,BSgenome.Scerevisiae.UCSC.sacCer1,BSgenome.Scerevisiae.UCSC.sacCer2,BSgenome.Scerevisiae.UCSC.sacCer3,BSgenome.Sscrofa.UCSC.susScr3,BSgenome.Sscrofa.UCSC.susScr3.masked,BSgenome.Tguttata.UCSC.taeGut1,BSgenome.Tguttata.UCSC.taeGut1.masked", "id": "BSgenome" }, "children": [ ] }, { "data": "cdf (126)", "attr": { "packageList": "agcdf,ath1121501cdf,barley1cdf,bovinecdf,bsubtiliscdf,canine2cdf,caninecdf,celeganscdf,chickencdf,citruscdf,cottoncdf,cyp450cdf,drosgenome1cdf,drosophila2cdf,ecoli2cdf,ecoliasv2cdf,ecolicdf,gahgu133acdf,gahgu133bcdf,gahgu133plus2cdf,gahgu95av2cdf,gahgu95bcdf,gahgu95ccdf,gahgu95dcdf,gahgu95ecdf,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 (155)", "attr": { "packageList": "adme16cod.db,ag.db,ath1121501.db,bovine.db,canine.db,canine2.db,celegans.db,chicken.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,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,mta10stprobeset.db,mta10sttranscriptcluster.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,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": "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 (3)", "attr": { "packageList": "MeSH.AOR.db,MeSH.db,MeSH.PCR.db", "id": "MeSHDb" }, "children": [ ] }, { "data": "OrganismDb (3)", "attr": { "packageList": "Homo.sapiens,Mus.musculus,Rattus.norvegicus", "id": "OrganismDb" }, "children": [ ] }, { "data": "OrgDb (19)", "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.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 (104)", "attr": { "packageList": "agprobe,ath1121501probe,barley1probe,bovineprobe,bsubtilisprobe,canine2probe,canineprobe,celegansprobe,chickenprobe,citrusprobe,cottonprobe,drosgenome1probe,drosophila2probe,ecoli2probe,ecoliasv2probe,ecoliprobe,gahgu133aprobe,gahgu133bprobe,gahgu133plus2probe,gahgu95av2probe,gahgu95bprobe,gahgu95cprobe,gahgu95dprobe,gahgu95eprobe,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,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 (1)", "attr": { "packageList": "SNPlocs.Hsapiens.dbSNP141.GRCh38", "id": "SNPlocs" }, "children": [ ] }, { "data": "TxDb (17)", "attr": { "packageList": "FDb.UCSC.tRNAs,TxDb.Athaliana.BioMart.plantsmart22,TxDb.Celegans.UCSC.ce6.ensGene,TxDb.Dmelanogaster.UCSC.dm3.ensGene,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.Mmusculus.UCSC.mm10.ensGene,TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Mmusculus.UCSC.mm9.knownGene,TxDb.Rnorvegicus.BioMart.igis,TxDb.Rnorvegicus.UCSC.rn4.ensGene,TxDb.Rnorvegicus.UCSC.rn5.refGene,TxDb.Scerevisiae.UCSC.sacCer2.sgdGene,TxDb.Scerevisiae.UCSC.sacCer3.sgdGene", "id": "TxDb" }, "children": [ ] } ] }, { "data": "SequenceAnnotation (3)", "attr": { "packageList": "miRNAtap.db,RmiR.Hs.miRNA,RmiR.hsa", "id": "SequenceAnnotation" }, "children": [ { "childnum": 0, "data": "GenomicSequence", "children": [ ] }, { "data": "miRNA (3)", "attr": { "packageList": "miRNAtap.db,RmiR.Hs.miRNA,RmiR.hsa", "id": "miRNA" }, "children": [ ] }, { "childnum": 0, "data": "MotifAnnotation", "children": [ ] } ] } ] }, { "data": "ExperimentData (223)", "attr": { "packageList": "affycompData,affydata,Affyhgu133A2Expr,Affyhgu133aExpr,Affyhgu133Plus2Expr,AffymetrixDataTestFiles,Affymoe4302Expr,airway,ALL,ALLMLL,AmpAffyExample,antiProfilesData,ARRmData,bcellViper,beadarrayExampleData,BeadArrayUseCases,beta7,bladderbatch,blimaTestingData,breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,bronchialIL13,bsseqData,cancerdata,CCl4,ccTutorial,ceu1kg,ceu1kgv,ceuhm3,cgdv17,ChAMPdata,charmData,cheung2010,ChimpHumanBrainData,chipenrich.data,ChIPXpressData,CLL,cMap2data,cnvGSAdata,COHCAPanno,colonCA,ConnectivityMap,COPDSexualDimorphism.data,CopyNumber450kData,COSMIC.67,CRCL18,curatedBladderData,curatedCRCData,curatedOvarianData,davidTiling,derfinderData,DeSousa2013,DLBCL,DMRcatedata,DonaPLLP2013,DREAM4,dressCheck,DrugVsDiseasedata,dsQTL,DvDdata,dyebiasexamples,EatonEtAlChIPseq,ecoliLeucine,encoDnaseI,estrogen,faahKO,fabiaData,facopy.annot,facsDorit,FANTOM3and4CAGE,ffpeExampleData,fibroEset,fission,Fletcher2013a,Fletcher2013b,flowFitExampleData,FlowSorted.Blood.450k,FlowSorted.DLPFC.450k,flowWorkspaceData,frmaExampleData,FunciSNP.data,gageData,gaschYHS,gatingMLData,gcspikelite,geneLenDataBase,GGdata,ggtut,golubEsets,GSBenchMark,GSVAdata,GWASdata,h5vcData,hapmap100khind,hapmap100kxba,hapmap500knsp,hapmap500ksty,hapmapsnp5,hapmapsnp6,harbChIP,HD2013SGI,healthyFlowData,HEEBOdata,hgu133abarcodevecs,hgu133plus2barcodevecs,hgu2beta7,HiCDataHumanIMR90,HiCDataLymphoblast,Hiiragi2013,HIVcDNAvantWout03,hmyriB36,HSMMSingleCell,humanStemCell,Illumina450ProbeVariants.db,IlluminaDataTestFiles,ind1KG,iontreeData,ITALICSData,Iyer517,JASPAR2014,KEGGandMetacoreDzPathwaysGEO,KEGGdzPathwaysGEO,kidpack,leeBamViews,leukemiasEset,LiebermanAidenHiC2009,ListerEtAlBSseq,lumiBarnes,LungCancerACvsSCCGEO,LungCancerLines,lungExpression,MafDb.ALL.wgs.phase1.release.v3.20101123,MafDb.ESP6500SI.V2.SSA137.dbSNP138,mammaPrintData,maqcExpression4plex,MAQCsubset,MAQCsubsetAFX,MAQCsubsetILM,MEDIPSData,MEEBOdata,metaMSdata,minfiData,miRNATarget,mitoODEdata,MMDiffBamSubset,mosaicsExample,mouse4302barcodevecs,MSBdata,msd16s,msdata,MUGAExampleData,Mulder2012,mvoutData,NCIgraphData,Neve2006,NGScopyData,parathyroid,parathyroidSE,pasilla,pasillaBamSubset,PathNetData,pcaGoPromoter.Hs.hg19,pcaGoPromoter.Mm.mm9,pcaGoPromoter.Rn.rn4,pd.atdschip.tiling,pepDat,phastCons100way.UCSC.hg19,ppiData,prebsdata,PREDAsampledata,ProData,pRolocdata,pumadata,PWMEnrich.Dmelanogaster.background,PWMEnrich.Hsapiens.background,PWMEnrich.Mmusculus.background,RforProteomics,rheumaticConditionWOLLBOLD,RIPSeekerData,RMassBankData,RNAinteractMAPK,RNAseqData.HNRNPC.bam.chr14,RnaSeqTutorial,RRBSdata,rRDPData,RUVnormalizeData,seqc,seqCNA.annot,serumStimulation,seventyGeneData,shinyMethylData,simpIntLists,SNAData,SNAGEEdata,SomatiCAData,SomaticCancerAlterations,SpikeIn,SpikeInSubset,stemHypoxia,stjudem,synapterdata,TargetScoreData,TargetSearchData,TBX20BamSubset,TCGAcrcmiRNA,TCGAcrcmRNA,TCGAMethylation450k,tinesath1cdf,tinesath1probe,tweeDEseqCountData,waveTilingData,XhybCasneuf,yeastCC,yeastExpData,yeastGSData,yeastNagalakshmi,yeastRNASeq,yri1kgv,zebrafishRNASeq", "id": "ExperimentData" }, "children": [ { "data": "Cancer (35)", "attr": { "packageList": "ALL,ALLMLL,antiProfilesData,bcellViper,bladderbatch,breastCancerMAINZ,breastCancerNKI,breastCancerTRANSBIG,breastCancerUNT,breastCancerUPP,breastCancerVDX,cancerdata,CLL,colonCA,COSMIC.67,curatedBladderData,curatedCRCData,curatedOvarianData,DLBCL,Fletcher2013a,Fletcher2013b,gageData,golubEsets,GSVAdata,HD2013SGI,kidpack,leukemiasEset,lungExpression,mammaPrintData,Neve2006,PREDAsampledata,ProData,seventyGeneData,SomaticCancerAlterations,stemHypoxia", "id": "Cancer" }, "children": [ { "data": "Breast (2)", "attr": { "packageList": "Neve2006,ProData", "id": "Breast" }, "children": [ ] }, { "data": "Colon (2)", "attr": { "packageList": "colonCA,HD2013SGI", "id": "Colon" }, "children": [ ] }, { "data": "Kidney (1)", "attr": { "packageList": "kidpack", "id": "Kidney" }, "children": [ ] }, { "data": "Leukemia (6)", "attr": { "packageList": "ALL,ALLMLL,CLL,golubEsets,GSVAdata,leukemiasEset", "id": "Leukemia" }, "children": [ ] }, { "data": "Lung (1)", "attr": { "packageList": "lungExpression", "id": "Lung" }, "children": [ ] }, { "data": "Ovarian (1)", "attr": { "packageList": "curatedOvarianData", "id": "Ovarian" }, "children": [ ] }, { "childnum": 0, "data": "Prostate", "children": [ ] } ] }, { "childnum": 0, "data": "CGH", "children": [ ] }, { "data": "ChIPchipData (1)", "attr": { "packageList": "ccTutorial", "id": "ChIPchipData" }, "children": [ ] }, { "data": "ChIPseqData (4)", "attr": { "packageList": "EatonEtAlChIPseq,MMDiffBamSubset,mosaicsExample,yeastNagalakshmi", "id": "ChIPseqData" }, "children": [ ] }, { "data": "EColiData (1)", "attr": { "packageList": "ecoliLeucine", "id": "EColiData" }, "children": [ ] }, { "data": "ExpressionData (4)", "attr": { "packageList": "ChAMPdata,ChimpHumanBrainData,RUVnormalizeData,seqc", "id": "ExpressionData" }, "children": [ ] }, { "childnum": 0, "data": "FlowCytData", "children": [ ] }, { "data": "HapMap (7)", "attr": { "packageList": "GGdata,hapmap100khind,hapmap100kxba,hapmap500knsp,hapmap500ksty,hapmapsnp5,hapmapsnp6", "id": "HapMap" }, "children": [ ] }, { "data": "HighThroughputSequencingData (9)", "attr": { "packageList": "ARRmData,dsQTL,geneLenDataBase,h5vcData,HiCDataHumanIMR90,HiCDataLymphoblast,HSMMSingleCell,seqc,tweeDEseqCountData", "id": "HighThroughputSequencingData" }, "children": [ ] }, { "data": "HIV (1)", "attr": { "packageList": "HIVcDNAvantWout03", "id": "HIV" }, "children": [ ] }, { "data": "MassSpectrometryData (7)", "attr": { "packageList": "faahKO,gcspikelite,metaMSdata,msdata,RforProteomics,RMassBankData,synapterdata", "id": "MassSpectrometryData" }, "children": [ ] }, { "childnum": 0, "data": "MethylseqData", "children": [ ] }, { "data": "NormalTissue (3)", "attr": { "packageList": "antiProfilesData,COPDSexualDimorphism.data,lumiBarnes", "id": "NormalTissue" }, "children": [ ] }, { "childnum": 0, "data": "Proteome", "children": [ ] }, { "childnum": 0, "data": "QualityAndTesting", "children": [ ] }, { "data": "RNAExpressionData (16)", "attr": { "packageList": "antiProfilesData,bladderbatch,blimaTestingData,ChimpHumanBrainData,COPDSexualDimorphism.data,curatedBladderData,curatedOvarianData,DREAM4,Fletcher2013a,Fletcher2013b,GSVAdata,lumiBarnes,mammaPrintData,seqc,seventyGeneData,TargetScoreData", "id": "RNAExpressionData" }, "children": [ ] }, { "data": "RNAseqData (19)", "attr": { "packageList": "airway,cheung2010,derfinderData,fission,GSVAdata,HSMMSingleCell,leeBamViews,parathyroid,parathyroidSE,pasilla,pasillaBamSubset,prebsdata,RNAseqData.HNRNPC.bam.chr14,RnaSeqTutorial,seqc,TBX20BamSubset,tweeDEseqCountData,yeastRNASeq,zebrafishRNASeq", "id": "RNAseqData" }, "children": [ ] }, { "childnum": 0, "data": "SpikeIns", "children": [ ] }, { "data": "StemCells (1)", "attr": { "packageList": "humanStemCell", "id": "StemCells" }, "children": [ ] }, { "data": "Yeast (10)", "attr": { "packageList": "davidTiling,EatonEtAlChIPseq,fission,gaschYHS,harbChIP,yeastCC,yeastExpData,yeastGSData,yeastNagalakshmi,yeastRNASeq", "id": "Yeast" }, "children": [ ] } ] } ]