{
  "_id": "6a1bd24e1d7bb097a0a14895",
  "Package": "multiWGCNA",
  "Type": "Package",
  "Title": "multiWGCNA",
  "Version": "1.11.0",
  "Authors@R": "c(\nperson(\"Dario\", \"Tommasini\", email=\"dtommasini0@gmail.com\",\nrole = c(\"aut\",\"cre\"),\ncomment = c(ORCID = \"0000-0002-1214-6547\")),\nperson(\"Brent\", \"Fogel\", role = c(\"aut\",\"ctb\")))",
  "Description": "An R package for deeping mining gene co-expression\nnetworks in multi-trait expression data. Provides functions for\nanalyzing, comparing, and visualizing WGCNA networks across\nconditions. multiWGCNA was designed to handle the common case\nwhere there are multiple biologically meaningful sample traits,\nsuch as disease vs wildtype across development or anatomical\nregion.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.2",
  "biocViews": "Sequencing, RNASeq, GeneExpression, DifferentialExpression,\nRegression, Clustering",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libuv1-dev libxml2-dev libx11-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:13 UTC",
  "RemoteUrl": "https://github.com/bioc/multiWGCNA",
  "RemoteRef": "HEAD",
  "RemoteSha": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:28:49 UTC",
    "User": "root"
  },
  "Author": "Dario Tommasini [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1214-6547>),\nBrent Fogel [aut, ctb]",
  "Maintainer": "Dario Tommasini <dtommasini0@gmail.com>",
  "MD5sum": "a06dac14fe726420a2ab4bba06e82a72",
  "_user": "bioc",
  "_type": "src",
  "_file": "multiWGCNA_1.11.0.tar.gz",
  "_fileid": "1e6b600526618169370081a305f3726d0620f2ccd06482dea32745320c929ab9",
  "_filesize": 4046750,
  "_sha256": "1e6b600526618169370081a305f3726d0620f2ccd06482dea32745320c929ab9",
  "_created": "2026-05-30T07:28:49.000Z",
  "_published": "2026-05-31T06:16:46.368Z",
  "_jobs": [
    {
      "job": 78703911722,
      "time": 231,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7314265173"
    },
    {
      "job": 78703911806,
      "time": 627,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306543263"
    },
    {
      "job": 78703911855,
      "time": 710,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306551957"
    },
    {
      "job": 78703911851,
      "time": 354,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307628157"
    },
    {
      "job": 78703911839,
      "time": 546,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307646957"
    },
    {
      "job": 78703911686,
      "time": 510,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306476204"
    },
    {
      "job": 78703911885,
      "time": 181,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306495877"
    },
    {
      "job": 78703911817,
      "time": 834,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7306564143"
    },
    {
      "job": 78703911747,
      "time": 1038,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7314347507"
    },
    {
      "job": 78703911836,
      "time": 535,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7306534268"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 1,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/multiWGCNA",
  "_commit": {
    "id": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381273
  },
  "_maintainer": {
    "name": "Dario Tommasini",
    "email": "dtommasini0@gmail.com",
    "login": "dariotommasini",
    "description": "Ph.D. student at UC Berkeley",
    "uuid": 103676484,
    "orcid": "0000-0002-1214-6547"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "ggalluvial",
      "role": "Depends"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "readr",
      "role": "Imports"
    },
    {
      "package": "WGCNA",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "flashClust",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "dcanr",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "ExperimentHub",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "vegan",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 1
    },
    {
      "week": "2025-25",
      "n": 1
    },
    {
      "week": "2025-34",
      "n": 2
    },
    {
      "week": "2025-35",
      "n": 2
    },
    {
      "week": "2025-48",
      "n": 2
    },
    {
      "week": "2026-01",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "sequencing",
    "rnaseq",
    "geneexpression",
    "differentialexpression",
    "regression",
    "clustering"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 346,
    "source": "https://www.bioconductor.org/packages/stats/bioc/multiWGCNA"
  },
  "_searchresults": 9,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/multiWGCNA.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "bidirectionalBestMatches",
    "BuildTOMFlowDF",
    "cleanDatExpr",
    "coexpressionLineGraph",
    "computeOverlapsFromWGCNA",
    "constructNetworks",
    "diffCoexpression",
    "diffModuleExpression",
    "drawMultiWGCNAnetwork",
    "GetDatExpr",
    "getModule",
    "getPreservation",
    "GetSignificantOverlap",
    "iterate",
    "makeTraitTable",
    "makeTraitTable2",
    "moduleComparisonPlot",
    "moduleExpressionPlot",
    "ModuleFlowPlot",
    "ModuleFlowPlot2Way",
    "moduleToModuleHeatmap",
    "name",
    "overlapComparisons",
    "performANOVA",
    "PlotMultiNodesTOMflow",
    "preservationComparisonPlot",
    "preservationComparisons",
    "PreservationPermutationTest",
    "PreservationScoreDistribution",
    "runDME",
    "summarizeResults",
    "TOMFlowPlot",
    "topNGenes"
  ],
  "_datasets": [
    {
      "name": "permutationTestResults",
      "title": "Permutation test results",
      "object": "permutationTestResults",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "bidirectionalBestMatches",
      "title": "Best matching modules",
      "topics": [
        "bidirectionalBestMatches"
      ]
    },
    {
      "page": "BuildTOMFlowDF",
      "title": "BuildTOMFlowDF",
      "topics": [
        "BuildTOMFlowDF"
      ]
    },
    {
      "page": "cleanDatExpr",
      "title": "cleanDatExpr",
      "topics": [
        "cleanDatExpr"
      ]
    },
    {
      "page": "coexpressionLineGraph",
      "title": "Coexpression Line Graph",
      "topics": [
        "coexpressionLineGraph"
      ]
    },
    {
      "page": "computeOverlapsFromWGCNA",
      "title": "computeOverlapsFromWGCNA",
      "topics": [
        "computeOverlapsFromWGCNA"
      ]
    },
    {
      "page": "constructNetworks",
      "title": "constructNetworks: Construct all the weighted gene correlation networks",
      "topics": [
        "constructNetworks"
      ]
    },
    {
      "page": "diffCoexpression",
      "title": "Differential co-expresison analysis",
      "topics": [
        "diffCoexpression"
      ]
    },
    {
      "page": "diffModuleExpression",
      "title": "Differential module expression",
      "topics": [
        "diffModuleExpression"
      ]
    },
    {
      "page": "drawMultiWGCNAnetwork",
      "title": "Draw multiWGCNA network",
      "topics": [
        "drawMultiWGCNAnetwork"
      ]
    },
    {
      "page": "GetDatExpr",
      "title": "Get expression data",
      "topics": [
        "GetDatExpr"
      ]
    },
    {
      "page": "getModule",
      "title": "name: Name of WGCNAobject",
      "topics": [
        "getModule"
      ]
    },
    {
      "page": "getPreservation",
      "title": "getPreservation",
      "topics": [
        "getPreservation"
      ]
    },
    {
      "page": "GetSignificantOverlap",
      "title": "Get significant overlap",
      "topics": [
        "GetSignificantOverlap"
      ]
    },
    {
      "page": "iterate",
      "title": "iterate: Iterate function across networks",
      "topics": [
        "iterate"
      ]
    },
    {
      "page": "makeTraitTable",
      "title": "Generate a trait table from a sample table",
      "topics": [
        "makeTraitTable"
      ]
    },
    {
      "page": "makeTraitTable2",
      "title": "Generate a trait table from a sample table (version 2)",
      "topics": [
        "makeTraitTable2"
      ]
    },
    {
      "page": "moduleComparisonPlot",
      "title": "Module comparison plot",
      "topics": [
        "moduleComparisonPlot"
      ]
    },
    {
      "page": "moduleExpressionPlot",
      "title": "Plots an expression profile for a module",
      "topics": [
        "moduleExpressionPlot"
      ]
    },
    {
      "page": "ModuleFlowPlot",
      "title": "Module sankey diagram",
      "topics": [
        "ModuleFlowPlot"
      ]
    },
    {
      "page": "ModuleFlowPlot2Way",
      "title": "Module sankey diagram",
      "topics": [
        "ModuleFlowPlot2Way"
      ]
    },
    {
      "page": "moduleToModuleHeatmap",
      "title": "Module to module heatmap",
      "topics": [
        "moduleToModuleHeatmap"
      ]
    },
    {
      "page": "name",
      "title": "name: Name of WGCNAobject",
      "topics": [
        "name"
      ]
    },
    {
      "page": "overlapComparisons",
      "title": "Overlap comparisons",
      "topics": [
        "overlapComparisons"
      ]
    },
    {
      "page": "performANOVA",
      "title": "Perform ANOVA",
      "topics": [
        "performANOVA"
      ]
    },
    {
      "page": "permutationTestResults",
      "title": "Permutation test results",
      "topics": [
        "permutationTestResults"
      ]
    },
    {
      "page": "PlotMultiNodesTOMflow",
      "title": "PlotMultiNodesTOMflow",
      "topics": [
        "PlotMultiNodesTOMflow"
      ]
    },
    {
      "page": "preservationComparisonPlot",
      "title": "Preservation Comparison Scatterplot",
      "topics": [
        "preservationComparisonPlot"
      ]
    },
    {
      "page": "preservationComparisons",
      "title": "Preservation comparisons",
      "topics": [
        "preservationComparisons"
      ]
    },
    {
      "page": "PreservationPermutationTest",
      "title": "PreservationPermutationTest",
      "topics": [
        "PreservationPermutationTest"
      ]
    },
    {
      "page": "PreservationScoreDistribution",
      "title": "PreservationScoreDistribution",
      "topics": [
        "PreservationScoreDistribution"
      ]
    },
    {
      "page": "runDME",
      "title": "Run differential module expression",
      "topics": [
        "runDME"
      ]
    },
    {
      "page": "summarizeResults",
      "title": "summarizeResults: Summarize results from a results list object",
      "topics": [
        "summarizeResults"
      ]
    },
    {
      "page": "TOMFlowPlot",
      "title": "TOMFlowPlot",
      "topics": [
        "TOMFlowPlot"
      ]
    },
    {
      "page": "topNGenes",
      "title": "topNGenes: Top N genes of a module",
      "topics": [
        "topNGenes"
      ]
    },
    {
      "page": "WGCNA-class",
      "title": "The WGCNA Class",
      "topics": [
        "WGCNA-class"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/multiWGCNA/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "checkmate",
    "circlize",
    "cli",
    "clipr",
    "cluster",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "crayon",
    "data.table",
    "dcanr",
    "DelayedArray",
    "digest",
    "doParallel",
    "doRNG",
    "dplyr",
    "dynamicTreeCut",
    "evaluate",
    "farver",
    "fastcluster",
    "fastmap",
    "flashClust",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "generics",
    "GenomicRanges",
    "ggalluvial",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "GlobalOptions",
    "glue",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "hms",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnet",
    "patchwork",
    "pillar",
    "pkgconfig",
    "plyr",
    "polyclip",
    "preprocessCore",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "readr",
    "reshape2",
    "rlang",
    "rmarkdown",
    "rngtools",
    "rpart",
    "rstudioapi",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shape",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "systemfonts",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tinytex",
    "tweenr",
    "tzdb",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "vroom",
    "WGCNA",
    "withr",
    "xfun",
    "XVector",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "astrocyte_map_v2.Rmd",
      "filename": "astrocyte_map_v2.html",
      "title": "multiWGCNA: visualizing condition-specific networks",
      "author": "Dario Tommasini",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Load multiWGCNA library",
        "Load astrocyte Ribotag RNA-seq data",
        "Network construction",
        "Compare modules by overlap",
        "Identify a module of interest",
        "Draw the multiWGCNA network",
        "Observe differential co-expression of top module genes",
        "Follow up with a preservation analysis",
        "Determining if preservation value is significant",
        "Conclusion"
      ],
      "created": "2023-06-06 22:53:50",
      "modified": "2025-11-26 17:53:08",
      "commits": 13
    },
    {
      "source": "autism_full_workflow.Rmd",
      "filename": "autism_full_workflow.html",
      "title": "multiWGCNA: the full workflow",
      "author": "Dario Tommasini",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Install the multiWGCNA R package",
        "Load microarray data from human post-mortem brains",
        "Perform network construction, module eigengene calculation, module-trait correlation",
        "Compare modules by overlap across conditions",
        "Perform differential module expression analysis",
        "Perform the module preservation analysis",
        "Summarize interesting results from the analyses",
        "Print the session info"
      ],
      "created": "2023-06-30 02:07:29",
      "modified": "2025-11-26 17:53:08",
      "commits": 13
    }
  ],
  "_score": 4.903089986991944,
  "_indexed": true,
  "_nocasepkg": "multiwgcna",
  "_universes": [
    "bioc",
    "dariotommasini"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T07:33:08.000Z",
      "distro": "noble",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "8f4b55c0c693b34dc16c6c52f4a7e73253b9b59876045d86def89eda0bd78774",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.11.0",
      "date": "2026-05-30T07:33:52.000Z",
      "distro": "noble",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "77bc69de8b176f8da7bcb3d29b24c612e7555f33b7a29d1fc14c23b9423aedf5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T10:43:52.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "cec814717df19fc00ef2af5e8627225946a1d0e76ce96808cbce7ddba528a931",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.11.0",
      "date": "2026-05-30T10:44:34.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "3149f9eeb963c3d0609f9d55ce5f2f4ceb770bf5fc4faa44f131a4f2d39c3b90",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.11.0",
      "date": "2026-05-30T07:32:31.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "6d009bf5d4bf3ef5ffa8dce28a7a9c261b4b086646223458c4a96db7da1ec5eb",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T07:35:52.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "ab520d190ad61c7843ae8db01327068d50ce7411849733ebc3582baf09e8e569",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-31T06:08:06.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "92daaab1e4f5a7437ae639449d0d616995726125d1b21d1154633287d944b77c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.11.0",
      "date": "2026-05-30T07:30:42.000Z",
      "commit": "928cc00af6b56cf2b79e192a9b58c301f2424f44",
      "fileid": "ede55c54678259a738dfaef5ffc63175fcd80e7b2cefa0ec5e2910711740853b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677922442"
    }
  ]
}