{
  "_id": "6ad92c46021a938ed758e05f",
  "Package": "RegEnrich",
  "Type": "Package",
  "Title": "Gene regulator enrichment analysis",
  "Version": "1.23.3",
  "Authors@R": "c(\nperson(\"Weiyang\", \"Tao\", email = \"weiyangtao1513@gmail.com\",\nrole = c(\"cre\", \"aut\")),\nperson(\"Aridaman\", \"Pandit\", email = \"A.Pandit@umcutrecht.nl\",\nrole = \"aut\"))",
  "Description": "This package is a pipeline to identify the key gene\nregulators in a biological process, for example in cell\ndifferentiation and in cell development after stimulation.\nThere are four major steps in this pipeline: (1) differential\nexpression analysis; (2) regulator-target network inference;\n(3) enrichment analysis; and (4) regulators scoring and\nranking.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "Collate": "'COEN.R' 'globals.R' 'DEA.R' 'GRN.R' 'data.R'\n'regenrichClasses.R' 'genericMethods.R' 'localUtils.R'\n'plots.R' 'regFET.R' 'regSEA.R' 'regenrich_diffExpr.R'\n'regenrich_enrich.R' 'regenrich_network.R'\n'regenrich_rankScore.R' 'results.R' 'show.R' 'topNet.R'",
  "biocViews": "GeneExpression, Transcriptomics, RNASeq, TwoChannel,\nTranscription, GeneTarget, NetworkEnrichment,\nDifferentialExpression, Network, NetworkInference,\nGeneSetEnrichment, FunctionalPrediction",
  "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-21 10:04:19 UTC",
  "RemoteUrl": "https://github.com/bioc/RegEnrich",
  "RemoteRef": "HEAD",
  "RemoteSha": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-21 21:04:14 UTC",
    "User": "root"
  },
  "Author": "Weiyang Tao [cre, aut],\nAridaman Pandit [aut]",
  "Maintainer": "Weiyang Tao <weiyangtao1513@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "RegEnrich_1.23.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/4f9052bf08d47806e2044267d81cc6cc3aef8283f316a5db07b5a4429cdd69b4",
  "_filesize": 1188939,
  "_sha256": "4f9052bf08d47806e2044267d81cc6cc3aef8283f316a5db07b5a4429cdd69b4",
  "_expires": "2027-01-29T21:18:58.000Z",
  "_created": "2026-10-21T21:04:14.000Z",
  "_published": "2026-10-21T21:19:02.205Z",
  "_upstream": "https://github.com/bioc/RegEnrich",
  "_status": "success",
  "_maintainer": {
    "name": "Weiyang Tao",
    "email": "weiyangtao1513@gmail.com",
    "login": "paodan",
    "description": "",
    "uuid": 29211054
  },
  "_jobs": [
    {
      "job": 119485411702,
      "time": 230,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382302455"
    },
    {
      "job": 119485411554,
      "time": 555,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12382507388"
    },
    {
      "job": 119485411623,
      "time": 444,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12381368624"
    },
    {
      "job": 119485411786,
      "time": 316,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12382658891"
    },
    {
      "job": 119485411587,
      "time": 210,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382757470"
    },
    {
      "job": 119480747735,
      "time": 566,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "12381472389"
    },
    {
      "job": 119485411603,
      "time": 164,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "12381506913"
    },
    {
      "job": 119485411809,
      "time": 270,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "12382426731"
    },
    {
      "job": 119485411899,
      "time": 367,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "12382990368"
    },
    {
      "job": 119485411820,
      "time": 360,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "12382406903"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 13
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595",
  "_commit": {
    "id": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
    "author": "Weiyang Tao <weiyangtao1513@gmail.com>",
    "committer": "Weiyang Tao <weiyangtao1513@gmail.com>",
    "message": "version bump 1.23.3\n",
    "time": 1792577059
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "role": "Depends"
    },
    {
      "package": "tibble",
      "role": "Depends"
    },
    {
      "package": "BiocSet",
      "role": "Depends"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Depends"
    },
    {
      "package": "randomForest",
      "role": "Imports"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "enrichit",
      "role": "Imports"
    },
    {
      "package": "qvalue",
      "role": "Imports"
    },
    {
      "package": "gson",
      "role": "Imports"
    },
    {
      "package": "DOSE",
      "role": "Imports"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "WGCNA",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 2.2.0",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Imports"
    },
    {
      "package": "GEOquery",
      "version": ">= 2.81.28",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    },
    {
      "week": "2026-19",
      "n": 2
    },
    {
      "week": "2026-41",
      "n": 1
    },
    {
      "week": "2026-43",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.23.2",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.22.1",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "geneexpression",
    "transcriptomics",
    "rnaseq",
    "twochannel",
    "transcription",
    "genetarget",
    "networkenrichment",
    "differentialexpression",
    "network",
    "networkinference",
    "genesetenrichment",
    "functionalprediction"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 479,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 472,
    "source": "https://www.bioconductor.org/packages/stats/bioc/RegEnrich"
  },
  "_mentions": 1,
  "_searchresults": 31,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/RegEnrich.html"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "%>%",
    "getResultsNames",
    "head",
    "newDeaSet",
    "newScore",
    "newTopNetwork",
    "plot_Enrich",
    "plotOrders",
    "plotRegTarExpr",
    "plotSoftPower",
    "regenrich_diffExpr",
    "regenrich_enrich",
    "regenrich_network",
    "regenrich_network<-",
    "regenrich_rankScore",
    "RegenrichSet",
    "results_DEA",
    "results_enrich",
    "results_expr",
    "results_score",
    "results_topNet",
    "show",
    "tail"
  ],
  "_datasets": [
    {
      "name": "Lyme_GSE63085",
      "title": "Example RNAseq dataset [Human]",
      "object": "Lyme_GSE63085",
      "file": "Lyme_GSE63085.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "TFs",
      "title": "Human gene regulators",
      "object": "TFs",
      "file": "TFs.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "TF",
        "TF_name"
      ],
      "rows": 1712,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "DeaSet-class",
      "title": "DeaSet class",
      "topics": [
        "DeaSet-class"
      ]
    },
    {
      "page": "dim-TopNetwork-method",
      "title": "dimention of `TopNetwork` object",
      "topics": [
        "dim,TopNetwork-method"
      ]
    },
    {
      "page": "Enrich-class",
      "title": "Enrich class",
      "topics": [
        "Enrich-class"
      ]
    },
    {
      "page": "getResultsNames",
      "title": "Inference the name of results of DESeq analysis by a formula (or model matrix) and sample information",
      "topics": [
        "getResultsNames"
      ]
    },
    {
      "page": "headTailScore",
      "title": "head or tail of Score object",
      "topics": [
        "head,Score-method",
        "tail,Score-method"
      ]
    },
    {
      "page": "Lyme_GSE63085",
      "title": "Example RNAseq dataset [Human]",
      "topics": [
        "Lyme_GSE63085"
      ]
    },
    {
      "page": "newDeaSet",
      "title": "DeaSet object creator",
      "topics": [
        "newDeaSet"
      ]
    },
    {
      "page": "newTopNetwork",
      "title": "TopNetwork object creator",
      "topics": [
        "newTopNetwork"
      ]
    },
    {
      "page": "plot_Enrich",
      "title": "Plot results of FET/GSEA enrichment analysis",
      "topics": [
        "plot_Enrich",
        "plot_Enrich,RegenrichSet-method"
      ]
    },
    {
      "page": "plotOrders",
      "title": "Compare the orders of two vectors",
      "topics": [
        "plotOrders"
      ]
    },
    {
      "page": "plotRegTarExpr",
      "title": "Plot regulator and its targets expression",
      "topics": [
        "plotRegTarExpr"
      ]
    },
    {
      "page": "plotSoftPower",
      "title": "Plot soft power for WGCNA analysis",
      "topics": [
        "plotSoftPower"
      ]
    },
    {
      "page": "print.Score",
      "title": "Print Score object",
      "topics": [
        "print.Score"
      ]
    },
    {
      "page": "regenrich_diffExpr",
      "title": "Differential expression analysis step",
      "topics": [
        "regenrich_diffExpr",
        "regenrich_diffExpr,RegenrichSet-method"
      ]
    },
    {
      "page": "regenrich_enrich",
      "title": "Enrichment analysis step",
      "topics": [
        "regenrich_enrich",
        "regenrich_enrich,RegenrichSet-method"
      ]
    },
    {
      "page": "regenrich_network",
      "title": "Regulator-target network inference step",
      "topics": [
        "regenrich_network",
        "regenrich_network,RegenrichSet-method",
        "regenrich_network<-",
        "regenrich_network<-,RegenrichSet,data.frame-method",
        "regenrich_network<-,RegenrichSet,TopNetwork-method"
      ]
    },
    {
      "page": "regenrich_rankScore",
      "title": "Regulator scoring and ranking",
      "topics": [
        "regenrich_rankScore",
        "regenrich_rankScore,RegenrichSet-method"
      ]
    },
    {
      "page": "RegenrichSet",
      "title": "RegenrichSet object creator",
      "topics": [
        "RegenrichSet"
      ]
    },
    {
      "page": "RegenrichSet-class",
      "title": "RegenrichSet class",
      "topics": [
        "RegenrichSet-class"
      ]
    },
    {
      "page": "results_expr",
      "title": "Result accessor functions",
      "topics": [
        "results_DEA",
        "results_enrich",
        "results_expr",
        "results_score",
        "results_topNet"
      ]
    },
    {
      "page": "Score",
      "title": "Score class",
      "topics": [
        "newScore",
        "Score-class"
      ]
    },
    {
      "page": "methodsOfShow",
      "title": "methods of generic function \"show\"",
      "topics": [
        "show,DeaSet-method",
        "show,Enrich-method",
        "show,RegenrichSet-method",
        "show,Score-method",
        "show,TopNetwork-method"
      ]
    },
    {
      "page": "TFs",
      "title": "Human gene regulators",
      "topics": [
        "TFs"
      ]
    },
    {
      "page": "TopNetwork-class",
      "title": "TopNetwork class",
      "topics": [
        "TopNetwork-class"
      ]
    }
  ],
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "backports",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocGenerics",
    "BiocIO",
    "BiocManager",
    "BiocParallel",
    "BiocSet",
    "BiocStyle",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bookdown",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DESeq2",
    "digest",
    "doParallel",
    "DOSE",
    "dplyr",
    "dynamicTreeCut",
    "enrichit",
    "evaluate",
    "farver",
    "fastcluster",
    "fastmap",
    "fastmatch",
    "fgsea",
    "fontawesome",
    "foreach",
    "foreign",
    "formatR",
    "Formula",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "GO.db",
    "GOSemSim",
    "gridExtra",
    "gson",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "impute",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnet",
    "ontologyIndex",
    "openssl",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "preprocessCore",
    "purrr",
    "qvalue",
    "R6",
    "randomForest",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "reshape2",
    "rlang",
    "rmarkdown",
    "rpart",
    "RSQLite",
    "rstudioapi",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "WGCNA",
    "withr",
    "xfun",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "RegEnrich.Rmd",
      "filename": "RegEnrich.html",
      "title": "RegEnrich: an R package for gene regulator enrichment analysis",
      "author": "Weiyang Tao, Aridaman Pandit ",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "A quick example",
        "Including RegEnrich library",
        "Initializing RegenrichSet object",
        "Runing four major steps and obtaining results",
        "RegenrichSet object initialization",
        "The RegenrichSet object",
        "Input data",
        "Expression data",
        "Sample information",
        "Regulators",
        "Other parameters",
        "Differential expression analysis",
        "Use the parameters initialized in the RegenrichSet object",
        "Re-specify the parameters for differential expression analysis",
        "Regulator-target network inference",
        "COEN (based on WGCNA)",
        "GRN (based on random forest)",
        "User defined network",
        "Enrichment analysis",
        "Fisher's exact test (FET)",
        "Gene set enrichment analysis (GSEA)",
        "Regulator scoring and ranking",
        "Case studies",
        "Case 1: Microarray (single-channel) data",
        "Background",
        "Reading the data",
        "RegEnrich analysis",
        "Case 2: RNAseq read count data",
        "Session info",
        "References"
      ],
      "created": "2020-03-07 13:35:14",
      "modified": "2026-10-21 09:58:26",
      "commits": 9
    }
  ],
  "_score": 4.190331698170292,
  "_indexed": true,
  "_nocasepkg": "regenrich",
  "_universes": [
    "bioc",
    "paodan"
  ],
  "_previous": "1.23.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.23.3",
      "date": "2026-10-21T21:10:23.000Z",
      "distro": "resolute",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/a44d3a9acb3afcf0c437a9967a1263ae5d18174afa6facdfd2eeae68a1b4ee84",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.23.3",
      "date": "2026-10-21T21:09:16.000Z",
      "distro": "resolute",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/f53146acda58b3f923e82f7fc0ad4980d234e8603b226a62c12ea66030b87da7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.23.3",
      "date": "2026-10-21T21:14:55.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/f747b6f1d2d7ed5ae8c0ea06a1cb2b4d02555090c9c81e4309a67cdde6345f8b",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.23.3",
      "date": "2026-10-21T21:14:29.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/6827b591b4aab1163c4e8f474709f7b985a0b97ab52f61658443e8a6e113c2a9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.23.3",
      "date": "2026-10-21T21:07:48.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/9d493d99bb0845ebde816bc987f733be302035daf30f9643e948af4eb4f3b45c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.23.3",
      "date": "2026-10-21T21:06:30.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/2d0dc4f2d0cbe59591c10d717b4909830180d22939023ebb39b957ff8f8af9b2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.23.3",
      "date": "2026-10-21T21:06:59.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/ba6647f901429027c962642d1b674e0e69cbf16b4f1be43b3b2a5612f2e47942",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.23.3",
      "date": "2026-10-21T21:06:42.000Z",
      "commit": "c0cdec286abb4cce46391da89ba8c9bbe1ca6d69",
      "fileid": "https://r2.ropensci.org/71f12696cbf0f80f32362be574b090b59c926050824d0d0202ecf3002f2fb491",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/39674486595"
    }
  ]
}