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  {
    "data": "Software (615)",
    "children": [
      {
        "data": "Annotation (84)",
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            "data": "GO (19)",
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            ],
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              "packageList": "annaffy,annotate,Category,categoryCompare,clusterProfiler,gage,globaltest,GOFunction,goProfiles,GOSemSim,goseq,GOstats,mgsa,MmPalateMiRNA,pcaGoPromoter,RamiGO,ReportingTools,RNAither,rols"
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          },
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              "packageList": "annaffy,annotate,Category,categoryCompare,clusterProfiler,DART,domainsignatures,gage,gCMAP,gene2pathway,GlobalAncova,globaltest,GOFunction,GOSemSim,graphite,GSVA,joda,KEGGgraph,keggorthology,KEGGprofile,KEGGSOAP,LiquidAssociation,mgsa,miRNApath,MmPalateMiRNA,NCIgraph,nem,pathRender,qpgraph,ReactomePA,rsbml,SBMLR,sigaR,SPIA"
            }
          },
          {
            "data": "ProprietaryPlatforms (1)",
            "children": [

            ],
            "attr": {
              "id": "ProprietaryPlatforms",
              "packageList": "altcdfenvs"
            }
          },
          {
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            "attr": {
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              "packageList": "affycoretools,AffyExpress,annaffy,annmap,arrayQualityMetrics,ArrayTools,DynDoc,Harshlight,MmPalateMiRNA,R453Plus1Toolbox,rnaSeqMap,simpleaffy,SpeCond,xmapbridge,xmapcore"
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        ],
        "attr": {
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          "packageList": "AffyExpress,altcdfenvs,annaffy,annmap,annotate,AnnotationDbi,AnnotationForge,annotationTools,ArrayTools,biomaRt,BSgenome,Category,categoryCompare,ChIPpeakAnno,DAVIDQuery,domainsignatures,DOSE,ecolitk,ensemblVEP,ENVISIONQuery,FunciSNP,gaggle,gCMAP,genomes,GenomicFeatures,GenomicRanges,GOstats,iBBiG,IdMappingAnalysis,IdMappingRetrieval,KEGGSOAP,matchBox,miRNApath,PAnnBuilder,pdInfoBuilder,RBioinf,Resourcerer,Risa,RMAPPER,RNAither,rnaSeqMap,rols,simpleaffy,UniProt.ws,VariantAnnotation,xmapbridge,xmapcore"
        }
      },
      {
        "data": "AssayDomains (237)",
        "children": [
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            "data": "aCGH (9)",
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            ],
            "attr": {
              "id": "aCGH",
              "packageList": "Clonality,gaia,KCsmart,mBPCR,pint,RCASPAR,sigaR,Vega,VegaMC"
            }
          },
          {
            "data": "CellBasedAssays (27)",
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            ],
            "attr": {
              "id": "CellBasedAssays",
              "packageList": "cellGrowth,cellHTS,cellHTS2,CellNOptR,ChemmineR,CNORdt,CNORode,coRNAi,flowCore,flowFP,flowPlots,flowQ,flowStats,flowUtils,flowViz,fmcsR,HTSanalyzeR,imageHTS,PANR,phenoDist,plateCore,prada,QUALIFIER,RNAinteract,RNAither,RTCA,staRank"
            }
          },
          {
            "data": "ChIPchip (6)",
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            ],
            "attr": {
              "id": "ChIPchip",
              "packageList": "ChIPpeakAnno,ChIPXpress,iChip,les,MotIV,rGADEM"
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          },
          {
            "data": "CopyNumberVariants (31)",
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            "attr": {
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              "packageList": "aCGH,ADaCGH2,beadarraySNP,CGHbase,cghMCR,Clonality,cn.farms,cn.mops,CNAnorm,CNTools,crlmm,DNAcopy,exomeCopy,fastseg,gaia,GLAD,HMMcopy,ITALICS,KCsmart,MANOR,mBPCR,MinimumDistance,PREDA,quantsmooth,reb,SMAP,snapCGH,SNPchip,VanillaICE,Vega,VegaMC"
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          },
          {
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            "attr": {
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              "packageList": "HELP,MEDIPS,MEDME,methylumi,TurboNorm"
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          },
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            ],
            "attr": {
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              "packageList": "AffyExpress,affylmGUI,anota,ArrayTools,baySeq,betr,BGmix,bgx,BioNet,BitSeq,coGPS,copa,Cormotif,cqn,cummeRbund,daMA,DART,ddCt,DEDS,DEGraph,DEGseq,DESeq,DEXSeq,DFP,diffGeneAnalysis,DSS,DTA,EBarrays,EDASeq,edgeR,fabia,factDesign,flagme,gage,genefu,GeneGroupAnalysis,GeneSelectMMD,GeneSelector,GlobalAncova,globaltest,gprege,GSRI,HEM,HTqPCR,IsoGeneGUI,lapmix,les,limma,limmaGUI,lmdme,LMGene,logitT,LPE,maanova,macat,maigesPack,manta,maSigPro,MEDIPS,MergeMaid,metaArray,metahdep,miRNApath,MmPalateMiRNA,Mulcom,multtest,netresponse,NOISeq,nudge,OCplus,oligo,oneChannelGUI,OrderedList,pcot2,phenoTest,pickgene,pint,plgem,PLPE,plw,puma,RankProd,Rcade,rnaSeqMap,ROC,SAGx,sigaR,siggenes,sigPathway,simpleaffy,snm,SpeCond,sscore,ssize,timecourse,tweeDEseq,twilight,waveTiling,webbioc,XDE,xps"
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          },
          {
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            "children": [

            ],
            "attr": {
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              "packageList": "bsseq,bumphunter,charm,HELP,les,lumi,MassArray,MEDIPS,MEDME,methVisual,methylumi,minfi,Repitools,TurboNorm,wateRmelon"
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          },
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            "data": "ExonArray (4)",
            "children": [

            ],
            "attr": {
              "id": "ExonArray",
              "packageList": "oligo,siggenes,snm,xps"
            }
          },
          {
            "data": "GeneExpression (59)",
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            ],
            "attr": {
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              "packageList": "affycoretools,AffyRNADegradation,AGDEX,anota,attract,BioNet,birta,BitSeq,categoryCompare,CoGAPS,cummeRbund,DART,ddCt,DEGseq,DTA,EasyqpcR,easyRNASeq,eisa,ExiMiR,ExpressionView,farms,ffpe,GeneExpressionSignature,genefu,GeneGA,GeneGroupAnalysis,GGtools,goseq,HTqPCR,HybridMTest,iBMQ,LiquidAssociation,manta,MiRaGE,Mulcom,netresponse,NormqPCR,oligo,pcaGoPromoter,pint,PREDA,PROMISE,qpcrNorm,qpgraph,RBioinf,Rcade,RCASPAR,ReadqPCR,Repitools,rnaSeqMap,RPA,safe,sigaR,siggenes,snm,tigre,trigger,waveTiling,xps"
            }
          },
          {
            "data": "GeneticVariability (14)",
            "children": [

            ],
            "attr": {
              "id": "GeneticVariability",
              "packageList": "beadarraySNP,chopsticks,CNVtools,deepSNV,GGtools,GWASTools,hapFabia,phyloseq,RLMM,SNPchip,snpStats,trigger,VanillaICE,VariantTools"
            }
          },
          {
            "data": "SNP (25)",
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            "attr": {
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          },
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            "data": "Transcription (24)",
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            "attr": {
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            }
          }
        ],
        "attr": {
          "id": "AssayDomains",
          "packageList": "lmdme"
        }
      },
      {
        "data": "AssayTechnologies (360)",
        "children": [
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            "data": "FlowCytometry (21)",
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            ],
            "attr": {
              "id": "FlowCytometry",
              "packageList": "flowClust,flowCore,flowFlowJo,flowFP,flowMeans,flowMerge,flowPhyto,flowPlots,flowQ,flowQB,flowStats,flowTrans,flowType,flowUtils,flowWorkspace,iFlow,ncdfFlow,plateCore,RchyOptimyx,SamSPECTRAL,spade"
            }
          },
          {
            "data": "HighThroughputSequencing (74)",
            "children": [
              {
                "data": "ChIPseq (23)",
                "children": [

                ],
                "attr": {
                  "id": "ChIPseq",
                  "packageList": "BayesPeak,ChIPpeakAnno,chipseq,ChIPseqR,ChIPsim,ChIPXpress,DBChIP,DESeq,DiffBind,DSS,edgeR,iASeq,iSeq,MEDIPS,mosaics,MotIV,NarrowPeaks,nucleR,PICS,QuasR,Rcade,rGADEM,triform"
                }
              },
              {
                "data": "Methylseq (3)",
                "children": [

                ],
                "attr": {
                  "id": "Methylseq",
                  "packageList": "MEDIPS,QuasR,Repitools"
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              },
              {
                "data": "RNAseq (23)",
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                ],
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                  "packageList": "ArrayExpressHTS,BitSeq,cqn,cummeRbund,DEGseq,DESeq,DEXSeq,DSS,easyRNASeq,EDASeq,edgeR,gage,goseq,iASeq,manta,MiRaGE,NOISeq,oneChannelGUI,QuasR,ReportingTools,rnaSeqMap,TSSi,tweeDEseq"
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            "attr": {
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          },
          {
            "data": "MassSpectrometry (17)",
            "children": [

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            "attr": {
              "id": "MassSpectrometry",
              "packageList": "apComplex,BRAIN,CAMERA,flagme,iontree,MassArray,MassSpecWavelet,MSnbase,mzR,PROcess,Rdisop,Risa,RMassBank,rols,rTANDEM,synapter,xcms"
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          },
          {
            "data": "Microarray (241)",
            "children": [
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                "data": "MultiChannel (2)",
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                ],
                "attr": {
                  "id": "MultiChannel",
                  "packageList": "aroma.light,snm"
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              },
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                "data": "OneChannel (55)",
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                "attr": {
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                  "packageList": "ABarray,affy,affycomp,affycoretools,AffyExpress,affyILM,affylmGUI,affypdnn,affyPLM,AffyRNADegradation,Agi4x44PreProcess,altcdfenvs,annaffy,annmap,aroma.light,ArrayExpress,arrayQualityMetrics,ArrayTools,beadarray,BrainStars,clippda,codelink,copa,ExiMiR,gage,gcrma,GeneRegionScan,GEOquery,GlobalAncova,globaltest,lapmix,limma,lmdme,lumi,makecdfenv,oligo,oneChannelGUI,PADOG,plw,PROMISE,puma,pvac,RefPlus,RLMM,SAGx,simpleaffy,SNAGEE,snm,tilingArray,TurboNorm,virtualArray,vsn,webbioc,xmapcore,xps"
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              },
              {
                "data": "TwoChannel (39)",
                "children": [

                ],
                "attr": {
                  "id": "TwoChannel",
                  "packageList": "aroma.light,ArrayExpress,arrayQualityMetrics,beadarraySNP,convert,copa,daMA,dyebias,gage,genArise,GEOquery,HELP,limma,limmaGUI,lmdme,lumi,maigesPack,MANOR,marray,methylumi,minfi,MmPalateMiRNA,nnNorm,nudge,oligo,OLIN,OLINgui,PADOG,plw,rama,SMAP,SNAGEE,snapCGH,snm,spotSegmentation,stepNorm,TurboNorm,vsn,wateRmelon"
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            "attr": {
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          },
          {
            "data": "MicrotitrePlateAssay (11)",
            "children": [
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                "data": "qPCR (6)",
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                ],
                "attr": {
                  "id": "qPCR",
                  "packageList": "ddCt,EasyqpcR,HTqPCR,NormqPCR,ReadqPCR,SLqPCR"
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            ],
            "attr": {
              "id": "MicrotitrePlateAssay",
              "packageList": "cellGrowth,ChemmineR,ddCt,fmcsR,HTqPCR,NormqPCR,ReadqPCR,SLqPCR,splots,staRank"
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            "data": "SAGE (7)",
            "children": [

            ],
            "attr": {
              "id": "SAGE",
              "packageList": "baySeq,DESeq,edgeR,GEOquery,MiRaGE,rnaSeqMap,sagenhaft"
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          },
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            "data": "Sequencing (36)",
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            "attr": {
              "id": "Sequencing",
              "packageList": "ArrayExpressHTS,Biostrings,birta,cn.mops,CNAnorm,CorMut,DBChIP,DECIPHER,deepSNV,exomeCopy,GenomicRanges,girafe,hapFabia,HiTC,HMMcopy,mcaGUI,MEDIPS,MiRaGE,mosaics,nucleR,PICS,qrqc,r3Cseq,Rcade,REDseq,ReQON,rGADEM,Rolexa,Rsamtools,rSFFreader,Rsubread,seqbias,ShortRead,triform,TSSi,VariantAnnotation"
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          }
        ],
        "attr": {
          "id": "AssayTechnologies",
          "packageList": "spkTools"
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      },
      {
        "data": "Bioinformatics (395)",
        "children": [
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            "data": "Classification (32)",
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            "attr": {
              "id": "Classification",
              "packageList": "cancerclass,Clonality,clst,clstutils,CMA,CRImage,ctc,DirichletMultinomial,eisa,ExpressionView,fastseg,flowPhyto,gene2pathway,genefu,gpls,iterativeBMA,logicFS,made4,maigesPack,MCRestimate,methVisual,MiPP,MLInterfaces,ontoCAT,pdmclass,phenoTest,phyloseq,procoil,RamiGO,RBioinf,rHVDM,Rmagpie"
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          },
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            "data": "Clustering (52)",
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            "attr": {
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          },
          {
            "data": "Enrichment (14)",
            "children": [
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                "data": "GeneSetEnrichment (8)",
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                ],
                "attr": {
                  "id": "GeneSetEnrichment",
                  "packageList": "Category,clusterProfiler,domainsignatures,gage,GOFunction,GSVA,iBBiG,mgsa"
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              },
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                  "packageList": "BioNet,DEGraph,gene2pathway,ibh,miRNApath,SPIA"
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            ],
            "attr": {
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              "packageList": "BioNet,Category,clusterProfiler,DEGraph,domainsignatures,gage,gene2pathway,GOFunction,GSVA,iBBiG,ibh,mgsa,miRNApath,SPIA"
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            ],
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          },
          {
            "data": "Networks (24)",
            "children": [
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                "data": "NetworkAnalysis (15)",
                "children": [

                ],
                "attr": {
                  "id": "NetworkAnalysis",
                  "packageList": "BioNet,DEGraph,GOSemSim,GraphAlignment,GraphAT,LiquidAssociation,minet,netresponse,PCpheno,ppiStats,RBGL,rsbml,SBMLR,SLGI,SQUADD"
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                "data": "NetworkInference (9)",
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                "attr": {
                  "id": "NetworkInference",
                  "packageList": "apComplex,GRENITS,joda,minet,PANR,predictionet,qpgraph,rHVDM,ScISI"
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            "attr": {
              "id": "Networks",
              "packageList": "RedeR"
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          },
          {
            "data": "Preprocessing (94)",
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            "attr": {
              "id": "Preprocessing",
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            }
          },
          {
            "data": "QualityControl (55)",
            "children": [

            ],
            "attr": {
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              "packageList": "AffyExpress,affylmGUI,affyPLM,AffyRNADegradation,altcdfenvs,arrayMvout,arrayQualityMetrics,ArrayTools,beadarray,clstutils,cummeRbund,DECIPHER,dyebias,EDASeq,farms,ffpe,flowPhyto,GWASTools,Harshlight,HELP,HTqPCR,ibh,limma,limmaGUI,lumi,MANOR,manta,mdqc,MEDIPS,methylumi,minfi,MmPalateMiRNA,OLIN,OLINgui,oneChannelGUI,OSAT,phyloseq,pvac,qrqc,R453Plus1Toolbox,rama,RBioinf,ReQON,RNAinteract,RNAither,Rolexa,RPA,ShortRead,simpleaffy,SNAGEE,snm,spikeLI,spotSegmentation,TEQC,wateRmelon"
            }
          },
          {
            "data": "SequenceMatching (13)",
            "children": [
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                "data": "MotifDiscovery (3)",
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                ],
                "attr": {
                  "id": "MotifDiscovery",
                  "packageList": "BCRANK,motifRG,rGADEM"
                }
              }
            ],
            "attr": {
              "id": "SequenceMatching",
              "packageList": "Biostrings,BSgenome,FunciSNP,hapFabia,microRNA,MmPalateMiRNA,motifStack,PWMEnrich,REDseq,seqLogo"
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          },
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            "data": "TimeCourse (17)",
            "children": [

            ],
            "attr": {
              "id": "TimeCourse",
              "packageList": "betr,cellGrowth,CellNOptR,CNORdt,CNORode,GeneGroupAnalysis,gprege,GRENITS,limma,LiquidAssociation,maSigPro,Mfuzz,RTCA,TDARACNE,tigre,timecourse,waveTiling"
            }
          },
          {
            "data": "Visualization (99)",
            "children": [
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                "data": "NetworkVisualization (11)",
                "children": [

                ],
                "attr": {
                  "id": "NetworkVisualization",
                  "packageList": "biocGraph,gaggle,hyperdraw,KEGGgraph,keggorthology,PANR,pathRender,RamiGO,RCytoscape,RedeR,Rgraphviz"
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zebrafishcdf,zebrafishprobe"
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