{
  "_id": "6aca88cefe5cc25786e8b0e0",
  "Package": "viper",
  "Version": "1.47.0",
  "Date": "2013-04-09",
  "Title": "Virtual Inference of Protein-activity by Enriched Regulon\nanalysis",
  "Author": "Mariano J Alvarez <reef103@gmail.com>",
  "Maintainer": "Mariano J Alvarez <reef103@gmail.com>",
  "Description": "Inference of protein activity from gene expression data,\nincluding the VIPER and msVIPER algorithms",
  "License": "file LICENSE",
  "biocViews": "SystemsBiology, NetworkEnrichment, GeneExpression,\nFunctionalPrediction, GeneRegulation",
  "Encoding": "UTF-8",
  "RoxygenNote": "6.1.1",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:51 UTC",
  "RemoteUrl": "https://github.com/bioc/viper",
  "RemoteRef": "HEAD",
  "RemoteSha": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-10 17:25:33 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "viper_1.47.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/c22f1aeff1e1b6030d829b941d21ddfc09536c53207c0d19946eae905387c243",
  "_filesize": 491978,
  "_sha256": "c22f1aeff1e1b6030d829b941d21ddfc09536c53207c0d19946eae905387c243",
  "_expires": "2027-01-18T18:49:48.000Z",
  "_created": "2026-10-10T17:25:33.000Z",
  "_published": "2026-10-10T18:49:50.156Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 1,
    "warning": 7,
    "note": 15
  },
  "_upstream": "https://github.com/bioc/viper",
  "_commit": {
    "id": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
    "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": 1777379931
  },
  "_maintainer": {
    "name": "Mariano J Alvarez",
    "email": "reef103@gmail.com",
    "login": "reef103",
    "description": "",
    "uuid": 31012433
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 114270279777,
      "time": 155,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11677237402"
    },
    {
      "job": 114270279798,
      "time": 253,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11676643809"
    },
    {
      "job": 114270279782,
      "time": 285,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11676728715"
    },
    {
      "job": 114270279765,
      "time": 223,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11678761760"
    },
    {
      "job": 114270279771,
      "time": 226,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11679417202"
    },
    {
      "job": 114269063732,
      "time": 361,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11676558560"
    },
    {
      "job": 114270279868,
      "time": 128,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11676813362"
    },
    {
      "job": 114270279862,
      "time": 217,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "11676898212"
    },
    {
      "job": 114270279795,
      "time": 195,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "11677038048"
    },
    {
      "job": 114270279769,
      "time": 199,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11676678569"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.14.0",
      "role": "Depends"
    },
    {
      "package": "Biobase",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "mixtools",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "e1071",
      "role": "Imports"
    },
    {
      "package": "KernSmooth",
      "role": "Imports"
    },
    {
      "package": "bcellViper",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.47.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.46.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "systemsbiology",
    "networkenrichment",
    "geneexpression",
    "functionalprediction",
    "generegulation"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 2018,
    "source": "https://www.bioconductor.org/packages/stats/bioc/viper"
  },
  "_mentions": 9,
  "_searchresults": 569,
  "_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/viper.html",
    "LICENSE"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "approxk2d",
    "aracne2regulon",
    "aracne2regulon4cnv",
    "aREA",
    "bootstrapmsviper",
    "bootstrapTtest",
    "distMode",
    "fcvarna",
    "filterColMatrix",
    "filterCV",
    "filterRowMatrix",
    "frcv",
    "frvarna",
    "integrateSignatures",
    "ledge",
    "msviper",
    "msviperAnnot",
    "msviperClass",
    "msviperCombinatorial",
    "msviperSynergy",
    "pruneRegulon",
    "rowTtest",
    "scaleGroups",
    "shadow",
    "signatureDistance",
    "ttestNull",
    "viper",
    "viperRPT",
    "viperSignature",
    "viperSimilarity"
  ],
  "_help": [
    {
      "page": "aecdf",
      "title": "Approximate empirical commulative distribution function",
      "topics": [
        "aecdf"
      ]
    },
    {
      "page": "approxk2d",
      "title": "approxk2d",
      "topics": [
        "approxk2d"
      ]
    },
    {
      "page": "aracne2regulon",
      "title": "Regulon object generation from ARACNe results",
      "topics": [
        "aracne2regulon"
      ]
    },
    {
      "page": "aracne2regulon4cnv",
      "title": "Regulon object generation from ARACNe results corrected by cnv",
      "topics": [
        "aracne2regulon4cnv"
      ]
    },
    {
      "page": "aREA",
      "title": "analytic Rank-based Enrichment Analysis",
      "topics": [
        "aREA"
      ]
    },
    {
      "page": "as.dist.signatureDistance",
      "title": "Distance matrix from signatureDistance objects",
      "topics": [
        "as.dist.signatureDistance"
      ]
    },
    {
      "page": "bootstrapmsviper",
      "title": "msviper bootstraps integration",
      "topics": [
        "bootstrapmsviper"
      ]
    },
    {
      "page": "bootstrapTtest-methods",
      "title": "Bootstrapped signature by t-test",
      "topics": [
        "bootstrapTtest",
        "bootstrapTtest,ExpressionSet-method",
        "bootstrapTtest,matrix-method"
      ]
    },
    {
      "page": "bootstrapViper",
      "title": "bootstrapsViper",
      "topics": [
        "bootstrapViper"
      ]
    },
    {
      "page": "comNames",
      "title": "Combinatorial annotation",
      "topics": [
        "comNames"
      ]
    },
    {
      "page": "distMode",
      "title": "Mode of continuous distributions",
      "topics": [
        "distMode"
      ]
    },
    {
      "page": "fcvarna",
      "title": "Variance of columns for arrays with NA values",
      "topics": [
        "fcvarna"
      ]
    },
    {
      "page": "filterColMatrix",
      "title": "Filter for columns of a matrix with no loss of col and row names",
      "topics": [
        "filterColMatrix"
      ]
    },
    {
      "page": "filterCV-methods",
      "title": "Coefficient of variation filter",
      "topics": [
        "filterCV",
        "filterCV,ExpressionSet-method",
        "filterCV,matrix-method"
      ]
    },
    {
      "page": "filterRowMatrix",
      "title": "Filter for rows of a matrix with no loss of col and row names",
      "topics": [
        "filterRowMatrix"
      ]
    },
    {
      "page": "frcv",
      "title": "Coeficient of variations for rows",
      "topics": [
        "frcv"
      ]
    },
    {
      "page": "frvarna",
      "title": "Variance of rows for arrays with NA values",
      "topics": [
        "frvarna"
      ]
    },
    {
      "page": "groupPwea3",
      "title": "Proportionally Weighted Enrichment Analysis for gene-set groups",
      "topics": [
        "groupPwea3"
      ]
    },
    {
      "page": "integrateSignatures",
      "title": "Integrate signatures",
      "topics": [
        "integrateSignatures"
      ]
    },
    {
      "page": "ledge",
      "title": "Leading-edge analysis",
      "topics": [
        "ledge"
      ]
    },
    {
      "page": "loadExpset",
      "title": "Loading expression sets",
      "topics": [
        "loadExpset"
      ]
    },
    {
      "page": "msviper",
      "title": "msVIPER",
      "topics": [
        "msviper"
      ]
    },
    {
      "page": "msviper-class",
      "title": "The msviper class",
      "topics": [
        "msviper-class"
      ]
    },
    {
      "page": "msviperAnnot",
      "title": "msVIPER annotation change",
      "topics": [
        "msviperAnnot"
      ]
    },
    {
      "page": "msviperClass",
      "title": "msVIPER class",
      "topics": [
        "msviperClass"
      ]
    },
    {
      "page": "msviperCombinatorial",
      "title": "msviper combinatorial analysis",
      "topics": [
        "msviperCombinatorial"
      ]
    },
    {
      "page": "msviperSynergy",
      "title": "msviper synergy analysis",
      "topics": [
        "msviperSynergy"
      ]
    },
    {
      "page": "plot.msviper",
      "title": "Plot msviper results",
      "topics": [
        "plot.msviper"
      ]
    },
    {
      "page": "pruneRegulon",
      "title": "Prune Regulons",
      "topics": [
        "pruneRegulon"
      ]
    },
    {
      "page": "pwea3NULLf",
      "title": "Null model function",
      "topics": [
        "pwea3NULLf"
      ]
    },
    {
      "page": "pwea3NULLgroups",
      "title": "Regulon-specific NULL model",
      "topics": [
        "pwea3NULLgroups"
      ]
    },
    {
      "page": "regulon-class",
      "title": "The regulon class",
      "topics": [
        "regulon-class"
      ]
    },
    {
      "page": "rowTtest-methods",
      "title": "Student's t-test for rows",
      "topics": [
        "rowTtest",
        "rowTtest,ExpressionSet-method",
        "rowTtest,matrix-method"
      ]
    },
    {
      "page": "scale.signatureDistance",
      "title": "Scaling of signatureDistance objects",
      "topics": [
        "scale.signatureDistance"
      ]
    },
    {
      "page": "scaleGroups",
      "title": "Signatures with grouping variable",
      "topics": [
        "scaleGroups"
      ]
    },
    {
      "page": "shadow",
      "title": "Shadow analysis for msviper objects",
      "topics": [
        "shadow"
      ]
    },
    {
      "page": "shadowRegulon",
      "title": "Correction for pleiotropy",
      "topics": [
        "shadowRegulon"
      ]
    },
    {
      "page": "signatureDistance",
      "title": "Signature Distance",
      "topics": [
        "signatureDistance"
      ]
    },
    {
      "page": "signatureDistance-class",
      "title": "signatureDistance",
      "topics": [
        "signatureDistance-class"
      ]
    },
    {
      "page": "sigT",
      "title": "Sigmoid transformation",
      "topics": [
        "sigT"
      ]
    },
    {
      "page": "summary.msviper",
      "title": "List msviper results",
      "topics": [
        "summary.msviper"
      ]
    },
    {
      "page": "ttestNull-methods",
      "title": "Null model by sample permutation testing",
      "topics": [
        "ttestNull",
        "ttestNull,ExpressionSet-method",
        "ttestNull,matrix-method"
      ]
    },
    {
      "page": "viper",
      "title": "VIPER",
      "topics": [
        "viper"
      ]
    },
    {
      "page": "viperRPT",
      "title": "viperRPT",
      "topics": [
        "viperRPT"
      ]
    },
    {
      "page": "viperSignature-methods",
      "title": "Generic S4 method for signature and sample-permutation null model for VIPER",
      "topics": [
        "viperSignature",
        "viperSignature,ExpressionSet-method",
        "viperSignature,matrix-method"
      ]
    },
    {
      "page": "viperSignature-class",
      "title": "viperSignature",
      "topics": [
        "viperSignature-class"
      ]
    },
    {
      "page": "viperSimilarity",
      "title": "VIPER similarity",
      "topics": [
        "viperSimilarity"
      ]
    }
  ],
  "_rundeps": [
    "askpass",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "bslib",
    "cachem",
    "class",
    "cli",
    "cpp11",
    "crosstalk",
    "curl",
    "data.table",
    "digest",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "isoband",
    "jquerylib",
    "jsonlite",
    "kernlab",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "mixtools",
    "nlme",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "plotly",
    "promises",
    "proxy",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "segmented",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "viper.Rnw",
      "filename": "viper.pdf",
      "title": "Using VIPER",
      "engine": "utils::Sweave",
      "headings": [
        "Overview of VIPER",
        "Citation",
        "Installation of viper package",
        "Getting started",
        "Generating the regulon object",
        "Master Regulator Analysis performed by msVIPER",
        "Beyond msVIPER",
        "Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER)"
      ],
      "created": "2014-03-20 23:55:49",
      "modified": "2019-02-26 17:56:10",
      "commits": 5
    }
  ],
  "_score": 7.637525228133189,
  "_indexed": true,
  "_nocasepkg": "viper",
  "_universes": [
    "bioc",
    "reef103"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-10T17:28:33.000Z",
      "distro": "resolute",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/5494816318abc6dc8318c4392e7b65db900be7444646e887de6c8cf35081dad7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.47.0",
      "date": "2026-10-10T17:28:38.000Z",
      "distro": "resolute",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/7edc62d9aab7e525dcd449e1b58aedc8e65f3737b5ecd928c9a6c7683b79401c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-10T18:47:06.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/7a843d91c6ce551f160cceb3bcb9ba96b18877df0215e91d5fe97c0f82cc647c",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.47.0",
      "date": "2026-10-10T18:46:59.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/edb626b2c0be00c3b91c4edd3d79e8d43a7293ce71881ad1f577449b0e3661ce",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.47.0",
      "date": "2026-10-10T17:28:06.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/12f611070e97c1f66f57f3c8a4672c53df26265c15013b57d4c4e2ecec9ee859",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-10T17:26:56.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/7fffc03fa46863d2adb60e7d7912f8b15a0ca027c86c07a48b0d74b3ad24f9f4",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-10T17:26:48.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/33c0f3bc608538554675ab28e6d6c5f06e1bf57271bd63db2bc28ac7caffaf3a",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.47.0",
      "date": "2026-10-10T17:27:07.000Z",
      "commit": "5e67590fd0ecb4f20eb7d97abc5bc9436f6a0021",
      "fileid": "https://r2.ropensci.org/6d2fe740f4cde5567d80e3cac4abb5fcb1e130f60ab13e48c3de9639fad8c660",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38071266549"
    }
  ]
}