{
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  "Package": "hdWGCNA",
  "Title": "High-dimensional Weighted Gene Co-expression Network Analysis",
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  "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", , \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Sam\", \"Morabito\", , \"smorabit@uci.edu\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-7768-4856\")),\nperson(\"Zechuan\", \"Shi\", , \"zechuas@uci.edu\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-2844-5816\"))\n)",
  "Description": "hdWGCNA is an R package for performing weighted gene\nco-expression network analysis in high dimensional -omics such\nas single-cell RNA-seq or spatial transcriptomics. It provides\ntools for constructing metacells, building co-expression\nnetworks, computing module eigengenes, and performing various\ndownstream analyses including module trait correlation, module\npreservation, and transcription factor network analysis.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "URL": "https://zaoqu-liu.github.io/hdWGCNA/,\nhttps://github.com/Zaoqu-Liu/hdWGCNA",
  "BugReports": "https://github.com/Zaoqu-Liu/hdWGCNA/issues",
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  "Repository": "https://zaoqu-liu.r-universe.dev",
  "Date/Publication": "2026-01-24 06:17:08 UTC",
  "RemoteUrl": "https://github.com/Zaoqu-Liu/hdWGCNA",
  "RemoteRef": "main",
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  "Packaged": {
    "Date": "2026-05-24 09:17:56 UTC",
    "User": "root"
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  "Author": "Zaoqu Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-0452-742X>),\nSam Morabito [ctb] (ORCID: <https://orcid.org/0000-0002-7768-4856>),\nZechuan Shi [ctb] (ORCID: <https://orcid.org/0000-0002-2844-5816>)",
  "Maintainer": "Zaoqu Liu <liuzaoqu@163.com>",
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  "_created": "2026-05-24T09:17:56.000Z",
  "_published": "2026-05-24T09:25:21.591Z",
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    "AvgModuleExpr",
    "BinPseudotime",
    "CheckSeurat5",
    "CheckWGCNAName",
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    "EnrichrBarPlot",
    "EnrichrDotPlot",
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    "FindDifferentialRegulons",
    "FindDMEs",
    "FindMajorIsoforms",
    "GetActiveWGCNA",
    "GetActiveWGCNAName",
    "GetAvgModuleExpr",
    "GetDatExpr",
    "GetDegrees",
    "GetEnrichrRegulonTable",
    "GetEnrichrTable",
    "GetHubGenes",
    "GetMELoadings",
    "GetMEs",
    "GetMetacellObject",
    "GetMetacellParams",
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    "GetMotifs",
    "GetMotifScores",
    "GetMotifTargets",
    "GetMultiExpr",
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    "GetPFMList",
    "GetPowerTable",
    "GetRegulonScores",
    "GetTFEval",
    "GetTFNetwork",
    "GetTFRegulons",
    "GetTFTargetGenes",
    "GetTOM",
    "GetWGCNAGenes",
    "GetWGCNAParams",
    "HubGeneNetworkPlot",
    "MetacellsByGroups",
    "MetaspotsByGroups",
    "ModuleConnectivity",
    "ModuleCorrelogram",
    "ModuleCorrNetwork",
    "ModuleEigengenes",
    "ModuleExprScore",
    "ModuleFeaturePlot",
    "ModuleNetworkPlot",
    "ModulePreservation",
    "ModulePreservationNetRep",
    "ModuleRadarPlot",
    "ModuleRegulatoryHeatmap",
    "ModuleRegulatoryNetwork",
    "ModuleRegulatoryNetworkPlot",
    "ModuleTopologyBarplot",
    "ModuleTopologyHeatmap",
    "ModuleTraitCorrelation",
    "ModuleUMAPPlot",
    "MotifOverlapBarPlot",
    "MotifScan",
    "NormalizeMetacells",
    "OverlapBarPlot",
    "OverlapDotPlot",
    "OverlapModulesDEGs",
    "OverlapModulesMotifs",
    "PlotDendrogram",
    "PlotDifferentialRegulons",
    "PlotDMEsLollipop",
    "PlotDMEsVolcano",
    "PlotKMEs",
    "PlotModulePreservation",
    "PlotModulePreservationLollipop",
    "PlotModuleTraitCorrelation",
    "PlotModuleTrajectory",
    "PlotSoftPowers",
    "ProjectModules",
    "ReassignModules",
    "RegulonBarPlot",
    "RegulonScores",
    "ResetModuleColors",
    "ResetModuleNames",
    "RunEnrichr",
    "RunEnrichrRegulons",
    "RunHarmonyMetacells",
    "RunModuleUMAP",
    "RunPCAMetacells",
    "RunUMAPMetacells",
    "scale01",
    "ScaleMetacells",
    "SelectNetworkGenes",
    "SetActiveWGCNA",
    "SetAvgModuleExpr",
    "SetDatExpr",
    "SetDegrees",
    "SetEnrichrRegulonTable",
    "SetEnrichrTable",
    "SetMELoadings",
    "SetMEs",
    "SetMetacellObject",
    "SetMetacellParams",
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    "SetMotifs",
    "SetMotifScores",
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    "SetNetworkData",
    "SetPFMList",
    "SetPowerTable",
    "SetRegulonScores",
    "SetTFEval",
    "SetTFNetwork",
    "SetTFRegulons",
    "SetupForWGCNA",
    "SetWGCNAGenes",
    "SetWGCNAParams",
    "shuffle_points",
    "TestSoftPowers",
    "TestSoftPowersConsensus",
    "TFNetworkPlot",
    "TransferModuleGenome",
    "umap_theme"
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      "title": "",
      "object": "test_seurat",
      "class": [
        "Seurat"
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      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
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    {
      "page": "AssignTFRegulons",
      "title": "AssignTFRegulons",
      "topics": [
        "AssignTFRegulons"
      ]
    },
    {
      "page": "AvgModuleExpr",
      "title": "AverageModuleExpr",
      "topics": [
        "AvgModuleExpr"
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    },
    {
      "page": "BinPseudotime",
      "title": "BinPseudotime",
      "topics": [
        "BinPseudotime"
      ]
    },
    {
      "page": "check_inputs",
      "title": "Check inputs",
      "topics": [
        "check_inputs"
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    {
      "page": "CheckSeurat5",
      "title": "CheckSeurat5",
      "topics": [
        "CheckSeurat5"
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    {
      "page": "CheckWGCNAName",
      "title": "CheckWGCNAName",
      "topics": [
        "CheckWGCNAName"
      ]
    },
    {
      "page": "ComputeModuleEigengene",
      "title": "ComputeModuleEigengene",
      "topics": [
        "ComputeModuleEigengene"
      ]
    },
    {
      "page": "ConstructMetacells",
      "title": "ConstructMetacells",
      "topics": [
        "ConstructMetacells"
      ]
    },
    {
      "page": "ConstructMetaspots",
      "title": "ConstructMetaspots",
      "topics": [
        "ConstructMetaspots"
      ]
    },
    {
      "page": "ConstructNetwork",
      "title": "ConstructNetwork",
      "topics": [
        "ConstructNetwork"
      ]
    },
    {
      "page": "ConstructPseudobulk",
      "title": "ConstructPseudobulk",
      "topics": [
        "ConstructPseudobulk"
      ]
    },
    {
      "page": "ConstructTFNetwork",
      "title": "ConstructTFNetwork",
      "topics": [
        "ConstructTFNetwork"
      ]
    },
    {
      "page": "corSparse",
      "title": "Sparse matrix correlation",
      "topics": [
        "corSparse"
      ]
    },
    {
      "page": "DimPlotMetacells",
      "title": "DimPlotMetacells",
      "topics": [
        "DimPlotMetacells"
      ]
    },
    {
      "page": "DoHubGeneHeatmap",
      "title": "Plots gene expression of hub genes as a heatmap",
      "topics": [
        "DoHubGeneHeatmap"
      ]
    },
    {
      "page": "EnrichrBarPlot",
      "title": "EnrichrBarPlot",
      "topics": [
        "EnrichrBarPlot"
      ]
    },
    {
      "page": "EnrichrDotPlot",
      "title": "EnrichrDotPlot",
      "topics": [
        "EnrichrDotPlot"
      ]
    },
    {
      "page": "FindAllDMEs",
      "title": "FindAllDMEs",
      "topics": [
        "FindAllDMEs"
      ]
    },
    {
      "page": "FindDifferentialRegulons",
      "title": "FindDifferentialRegulons",
      "topics": [
        "FindDifferentialRegulons"
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    },
    {
      "page": "FindDMEs",
      "title": "FindDMEs",
      "topics": [
        "FindDMEs"
      ]
    },
    {
      "page": "FindMajorIsoforms",
      "title": "FindMajorIsoforms",
      "topics": [
        "FindMajorIsoforms"
      ]
    },
    {
      "page": "GetActiveWGCNA",
      "title": "GetActiveWGCNA",
      "topics": [
        "GetActiveWGCNA"
      ]
    },
    {
      "page": "GetActiveWGCNAName",
      "title": "GetActiveWGCNAName",
      "topics": [
        "GetActiveWGCNAName"
      ]
    },
    {
      "page": "GetAvgModuleExpr",
      "title": "GetAvgModuleExpr",
      "topics": [
        "GetAvgModuleExpr"
      ]
    },
    {
      "page": "GetDatExpr",
      "title": "GetDatExpr",
      "topics": [
        "GetDatExpr"
      ]
    },
    {
      "page": "GetDegrees",
      "title": "GetDegrees",
      "topics": [
        "GetDegrees"
      ]
    },
    {
      "page": "GetEnrichrRegulonTable",
      "title": "GetEnrichrRegulonTable",
      "topics": [
        "GetEnrichrRegulonTable"
      ]
    },
    {
      "page": "GetEnrichrTable",
      "title": "GetEnrichrTable",
      "topics": [
        "GetEnrichrTable"
      ]
    },
    {
      "page": "GetHubGenes",
      "title": "GetHubGenes",
      "topics": [
        "GetHubGenes"
      ]
    },
    {
      "page": "GetMELoadings",
      "title": "GetMELoadings",
      "topics": [
        "GetMELoadings"
      ]
    },
    {
      "page": "GetMEs",
      "title": "GetMEs",
      "topics": [
        "GetMEs"
      ]
    },
    {
      "page": "GetMetacellObject",
      "title": "GetMetacellObject",
      "topics": [
        "GetMetacellObject"
      ]
    },
    {
      "page": "GetMetacellParams",
      "title": "GetMetacellParams",
      "topics": [
        "GetMetacellParams"
      ]
    },
    {
      "page": "GetModulePreservation",
      "title": "GetModulePreservation",
      "topics": [
        "GetModulePreservation"
      ]
    },
    {
      "page": "GetModules",
      "title": "GetModules",
      "topics": [
        "GetModules"
      ]
    },
    {
      "page": "GetModuleScores",
      "title": "GetModuleScores",
      "topics": [
        "GetModuleScores"
      ]
    },
    {
      "page": "GetModuleTraitCorrelation",
      "title": "GetModuleTraitCorrelation",
      "topics": [
        "GetModuleTraitCorrelation"
      ]
    },
    {
      "page": "GetModuleUMAP",
      "title": "GetModuleUMAP",
      "topics": [
        "GetModuleUMAP"
      ]
    },
    {
      "page": "GetMotifMatrix",
      "title": "GetMotifMatrix",
      "topics": [
        "GetMotifMatrix"
      ]
    },
    {
      "page": "GetMotifOverlap",
      "title": "GetMotifOverlap",
      "topics": [
        "GetMotifOverlap"
      ]
    },
    {
      "page": "GetMotifs",
      "title": "GetMotifs",
      "topics": [
        "GetMotifs"
      ]
    },
    {
      "page": "GetMotifScores",
      "title": "GetMotifScores",
      "topics": [
        "GetMotifScores"
      ]
    },
    {
      "page": "GetMotifTargets",
      "title": "GetMotifTargets",
      "topics": [
        "GetMotifTargets"
      ]
    },
    {
      "page": "GetMultiExpr",
      "title": "GetMultiExpr",
      "topics": [
        "GetMultiExpr"
      ]
    },
    {
      "page": "GetNetworkData",
      "title": "GetNetworkData",
      "topics": [
        "GetNetworkData"
      ]
    },
    {
      "page": "GetPFMList",
      "title": "GetPFMList",
      "topics": [
        "GetPFMList"
      ]
    },
    {
      "page": "GetPowerTable",
      "title": "GetPowerTable",
      "topics": [
        "GetPowerTable"
      ]
    },
    {
      "page": "GetRegulonScores",
      "title": "GetRegulonScores",
      "topics": [
        "GetRegulonScores"
      ]
    },
    {
      "page": "GetTFEval",
      "title": "GetTFEval",
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      "page": "ModuleFeaturePlot",
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      "title": "ModulePreservationNetRep",
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      "page": "ModuleRadarPlot",
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