{
  "_id": "6a1acff31d7bb097a09e0f3e",
  "Package": "Pigengene",
  "Type": "Package",
  "Title": "Infers biological signatures from gene expression data",
  "Version": "1.39.0",
  "Date": "2016-03-31",
  "Author": "Habil Zare, Amir Foroushani, Rupesh Agrahari, Meghan Short,\nIsha Mehta, Neda Emami, and Sogand Sajedi",
  "Maintainer": "Habil Zare <zare@u.washington.edu>",
  "biocViews": "GeneExpression, RNASeq, NetworkInference, Network,\nGraphAndNetwork, BiomedicalInformatics, SystemsBiology,\nTranscriptomics, Classification, Clustering, DecisionTree,\nDimensionReduction, PrincipalComponent, Microarray,\nNormalization, ImmunoOncology",
  "Description": "Pigengene package provides an efficient way to infer\nbiological signatures from gene expression profiles. The\nsignatures are independent from the underlying platform, e.g.,\nthe input can be microarray or RNA Seq data. It can even infer\nthe signatures using data from one platform, and evaluate them\non the other. Pigengene identifies the modules (clusters) of\nhighly coexpressed genes using coexpression network analysis,\nsummarizes the biological information of each module in an\neigengene, learns a Bayesian network that models the\nprobabilistic dependencies between modules, and builds a\ndecision tree based on the expression of eigengenes.",
  "License": "GPL (>=2)",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:43:36 UTC",
  "RemoteUrl": "https://github.com/bioc/Pigengene",
  "RemoteRef": "HEAD",
  "RemoteSha": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
  "Packaged": {
    "Date": "2026-05-30 08:16:07 UTC",
    "User": "root"
  },
  "MD5sum": "f1c68db50786987eaf19e52f9d8591ee",
  "_user": "bioc",
  "_type": "src",
  "_file": "Pigengene_1.39.0.tar.gz",
  "_fileid": "49a98a3730e95257a787f5cf06d39b2c93526e5322baa2a80a1caff42ac4fcea",
  "_filesize": 2805130,
  "_sha256": "49a98a3730e95257a787f5cf06d39b2c93526e5322baa2a80a1caff42ac4fcea",
  "_created": "2026-05-30T08:16:07.000Z",
  "_published": "2026-05-30T11:54:27.039Z",
  "_jobs": [
    {
      "job": 78635999644,
      "time": 343,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306793493"
    },
    {
      "job": 78635999648,
      "time": 840,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306841210"
    },
    {
      "job": 78635999657,
      "time": 671,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306825610"
    },
    {
      "job": 78635999653,
      "time": 343,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7307981171"
    },
    {
      "job": 78635999640,
      "time": 372,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7307983310"
    },
    {
      "job": 78633077059,
      "time": 3388,
      "config": "source",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7306760247"
    },
    {
      "job": 78635999641,
      "time": 296,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306788600"
    },
    {
      "job": 78635999649,
      "time": 713,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7306829718"
    },
    {
      "job": 78635999646,
      "time": 719,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7306830323"
    },
    {
      "job": 78635999655,
      "time": 666,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306825200"
    }
  ],
  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 16
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098",
  "_status": "failure",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/Pigengene",
  "_commit": {
    "id": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
    "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": 1777380216
  },
  "_maintainer": {
    "name": "Habil Zare",
    "email": "zare@u.washington.edu"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.3",
      "role": "Depends"
    },
    {
      "package": "graph",
      "role": "Depends"
    },
    {
      "package": "BiocStyle",
      "version": ">= 2.28.0",
      "role": "Depends"
    },
    {
      "package": "bnlearn",
      "version": ">= 4.7",
      "role": "Imports"
    },
    {
      "package": "C50",
      "version": ">= 0.1.2",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "partykit",
      "role": "Imports"
    },
    {
      "package": "Rgraphviz",
      "role": "Imports"
    },
    {
      "package": "WGCNA",
      "role": "Imports"
    },
    {
      "package": "GO.db",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "version": ">= 1.0.8",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "gdata",
      "role": "Imports"
    },
    {
      "package": "clusterProfiler",
      "role": "Imports"
    },
    {
      "package": "ReactomePA",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "openxlsx",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "role": "Imports"
    },
    {
      "package": "DOSE",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "version": ">= 3.7.0",
      "role": "Suggests"
    },
    {
      "package": "org.Mm.eg.db",
      "version": ">= 3.7.0",
      "role": "Suggests"
    },
    {
      "package": "biomaRt",
      "version": ">= 2.30.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "AnnotationDbi",
      "role": "Suggests"
    },
    {
      "package": "energy",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-35",
      "n": 1
    },
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.39.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.38.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression",
    "rnaseq",
    "networkinference",
    "network",
    "graphandnetwork",
    "biomedicalinformatics",
    "systemsbiology",
    "transcriptomics",
    "classification",
    "clustering",
    "decisiontree",
    "dimensionreduction",
    "principalcomponent",
    "microarray",
    "normalization",
    "immunooncology"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 458,
    "source": "https://www.bioconductor.org/packages/stats/bioc/Pigengene"
  },
  "_mentions": 4,
  "_searchresults": 13,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/Pigengene.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "apply.filter",
    "balance",
    "calculate.beta",
    "check.nas",
    "check.pigengene.input",
    "combine.networks",
    "compact.tree",
    "compute.pigengene",
    "dcor.matrix",
    "determine.modules",
    "draw.bn",
    "gene.mapping",
    "get.enriched.pw",
    "get.fitted.leaf",
    "get.genes",
    "get.used.features",
    "learn.bn",
    "make.decision.tree",
    "make.filter",
    "message.if",
    "module.heatmap",
    "one.step.pigengene",
    "pheatmap.type",
    "plot.pigengene",
    "preds.at",
    "project.eigen",
    "pvalues.manova",
    "save.if",
    "wgcna.one.step"
  ],
  "_datasets": [
    {
      "name": "aml",
      "title": "AML gene expression profile",
      "object": "aml",
      "file": "aml.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "7180_at",
        "272_at",
        "2769_at",
        "4267_at",
        "79183_at",
        "25801_at",
        "23345_at",
        "10562_at",
        "11221_at",
        "154664_at",
        "10321_at",
        "10625_at",
        "2745_at",
        "23564_at",
        "118932_at",
        "660_at",
        "634_at",
        "4973_at",
        "5004_at",
        "55062_at",
        "6645_at",
        "29094_at",
        "8555_at",
        "820_at",
        "2322_at",
        "51441_at",
        "4350_at",
        "762_at",
        "89797_at",
        "6659_at",
        "4318_at",
        "29952_at",
        "54682_at",
        "84255_at",
        "51734_at",
        "440603_at",
        "1053_at",
        "9334_at",
        "9914_at",
        "7798_at",
        "23569_at",
        "144423_at",
        "2730_at",
        "5005_at",
        "414918_at",
        "1308_at",
        "7461_at",
        "3579_at",
        "57820_at",
        "2746_at",
        "3930_at",
        "64101_at",
        "1915_at",
        "3240_at",
        "8807_at",
        "3934_at",
        "999_at",
        "23401_at",
        "50807_at",
        "2356_at",
        "170463_at",
        "91252_at",
        "1183_at",
        "9440_at",
        "84641_at",
        "440104_at",
        "8445_at",
        "343990_at",
        "1116_at",
        "22906_at",
        "353189_at",
        "163882_at",
        "63910_at",
        "8993_at",
        "123920_at",
        "23046_at",
        "7277_at",
        "550643_at",
        "5318_at",
        "100506696_at",
        "6732_at",
        "64760_at",
        "1635_at",
        "6790_at",
        "51082_at",
        "84326_at",
        "120892_at",
        "29127_at",
        "266747_at",
        "7033_at",
        "84418_at",
        "85021_at",
        "960_at",
        "80853_at",
        "5214_at",
        "3728_at",
        "8778_at",
        "126917_at",
        "57787_at",
        "861_at",
        "80196_at",
        "79689_at",
        "84078_at",
        "25797_at",
        "285958_at",
        "26034_at",
        "306_at",
        "240_at",
        "55529_at",
        "5208_at",
        "150372_at",
        "3708_at",
        "79143_at",
        "4774_at",
        "1955_at",
        "9112_at",
        "65220_at",
        "5867_at",
        "26086_at",
        "100505481_at",
        "6809_at",
        "150726_at",
        "83478_at",
        "114971_at",
        "338339_at",
        "51361_at",
        "10284_at",
        "825_at",
        "65986_at",
        "11186_at",
        "84941_at",
        "55825_at",
        "10096_at",
        "129642_at",
        "983_at",
        "7443_at",
        "9848_at",
        "58484_at",
        "5495_at",
        "23604_at",
        "90850_at",
        "1454_at",
        "6919_at",
        "55605_at",
        "56965_at",
        "3678_at",
        "81855_at",
        "253018_at",
        "79971_at",
        "55553_at",
        "89874_at",
        "4070_at",
        "9741_at",
        "51477_at",
        "10154_at",
        "148534_at",
        "8895_at",
        "63939_at",
        "9922_at",
        "4628_at",
        "1084_at",
        "9987_at",
        "3727_at",
        "6729_at",
        "317671_at",
        "2057_at",
        "10970_at",
        "54946_at",
        "1536_at",
        "4288_at",
        "2040_at",
        "388341_at",
        "23261_at",
        "55621_at",
        "159_at",
        "3425_at",
        "2531_at",
        "6624_at",
        "1432_at",
        "199675_at",
        "383_at",
        "83986_at",
        "112950_at",
        "92912_at",
        "4680_at",
        "55635_at",
        "29890_at",
        "85027_at",
        "10608_at",
        "2230_at",
        "203328_at",
        "57666_at",
        "54443_at",
        "160760_at",
        "64400_at",
        "201799_at",
        "6840_at",
        "115350_at",
        "1058_at",
        "54941_at",
        "116362_at",
        "27245_at",
        "2067_at",
        "80331_at",
        "3087_at",
        "4332_at",
        "8407_at",
        "649_at",
        "6300_at",
        "5795_at",
        "49854_at",
        "100141515_at",
        "64386_at",
        "8972_at",
        "8897_at",
        "100506548_at",
        "10565_at",
        "6590_at",
        "2648_at",
        "10945_at",
        "29997_at",
        "996_at",
        "84275_at",
        "54830_at",
        "7702_at",
        "2762_at",
        "9764_at",
        "23549_at",
        "5562_at",
        "87_at",
        "196051_at",
        "60481_at",
        "54849_at",
        "51545_at",
        "8794_at",
        "50854_at",
        "5366_at",
        "1118_at",
        "2681_at",
        "26268_at",
        "688_at",
        "56265_at",
        "81027_at",
        "23654_at",
        "2215_at",
        "30061_at",
        "1371_at",
        "51379_at",
        "9655_at",
        "9926_at",
        "8476_at",
        "140465_at",
        "83461_at",
        "100_at",
        "100129460_at",
        "6484_at",
        "56931_at",
        "5819_at",
        "978_at",
        "10335_at",
        "10890_at",
        "1759_at",
        "83540_at",
        "2258_at",
        "26018_at",
        "5359_at",
        "129080_at",
        "9949_at",
        "3772_at",
        "121512_at",
        "64858_at",
        "64151_at",
        "2357_at",
        "259266_at",
        "701_at",
        "415116_at",
        "53346_at",
        "7750_at",
        "80896_at",
        "6158_at",
        "92906_at",
        "146857_at",
        "64754_at",
        "2114_at",
        "26191_at",
        "64078_at",
        "81619_at",
        "54850_at",
        "5313_at",
        "2153_at",
        "151556_at",
        "55194_at",
        "4311_at",
        "949_at",
        "51542_at",
        "57136_at",
        "57222_at",
        "22901_at",
        "91298_at",
        "2747_at",
        "6886_at",
        "3021_at",
        "7490_at",
        "163033_at",
        "10874_at",
        "203100_at",
        "390916_at",
        "59349_at",
        "56180_at",
        "10112_at",
        "91419_at",
        "3338_at",
        "2358_at",
        "2992_at",
        "57473_at",
        "63027_at",
        "51479_at",
        "7071_at",
        "90417_at",
        "8987_at",
        "178_at",
        "113263_at",
        "55700_at",
        "6947_at",
        "2593_at",
        "166_at",
        "256691_at",
        "6283_at",
        "738_at",
        "196385_at",
        "8218_at",
        "25852_at",
        "10116_at",
        "84986_at",
        "10804_at",
        "1062_at",
        "122769_at",
        "3482_at",
        "51099_at",
        "6576_at",
        "4048_at",
        "55872_at",
        "127687_at",
        "149951_at",
        "7068_at",
        "79887_at",
        "10362_at",
        "56977_at",
        "9562_at",
        "90550_at",
        "121441_at",
        "84678_at",
        "26253_at",
        "467_at",
        "80823_at",
        "613_at",
        "23598_at",
        "408_at",
        "53831_at",
        "6691_at",
        "260429_at",
        "23061_at",
        "56992_at",
        "7709_at",
        "5087_at",
        "123096_at",
        "8575_at",
        "60314_at",
        "1938_at",
        "57106_at",
        "8030_at",
        "22824_at",
        "51523_at",
        "79733_at",
        "55350_at",
        "819_at",
        "23492_at",
        "23243_at",
        "11338_at",
        "388272_at",
        "79674_at",
        "9379_at",
        "699_at",
        "3200_at",
        "55196_at",
        "79023_at",
        "8529_at",
        "3204_at",
        "10953_at",
        "26156_at",
        "7357_at",
        "7414_at",
        "51022_at",
        "25875_at",
        "10403_at",
        "221477_at",
        "23157_at",
        "1063_at",
        "953_at",
        "51275_at",
        "5900_at",
        "284904_at",
        "56729_at",
        "29028_at",
        "441150_at",
        "4794_at",
        "91748_at",
        "11031_at",
        "54726_at",
        "3684_at",
        "7153_at",
        "339287_at",
        "10217_at",
        "84973_at",
        "55048_at",
        "29968_at",
        "54963_at",
        "3161_at",
        "541565_at",
        "93624_at",
        "3577_at",
        "5110_at",
        "8560_at",
        "25870_at",
        "84248_at",
        "353116_at",
        "5037_at",
        "5600_at",
        "8767_at",
        "1153_at",
        "4317_at",
        "6241_at",
        "890_at",
        "164312_at",
        "84162_at",
        "22913_at",
        "375190_at",
        "11072_at",
        "28987_at",
        "210_at",
        "153830_at",
        "150468_at",
        "401577_at",
        "1088_at",
        "6708_at",
        "342892_at",
        "7812_at",
        "1316_at",
        "10107_at",
        "23228_at",
        "494143_at",
        "8349_at",
        "2077_at",
        "51611_at",
        "140803_at",
        "53829_at",
        "55702_at",
        "51177_at",
        "84267_at",
        "23764_at",
        "359948_at",
        "29089_at",
        "55789_at",
        "10827_at",
        "7130_at",
        "9700_at",
        "55466_at",
        "100505573_at",
        "6877_at",
        "170394_at",
        "151162_at",
        "60436_at",
        "27436_at",
        "55215_at",
        "5427_at",
        "80758_at",
        "8666_at",
        "54973_at",
        "8875_at",
        "9787_at",
        "10844_at",
        "84188_at",
        "353_at",
        "114915_at",
        "51078_at",
        "55711_at",
        "10762_at",
        "9978_at",
        "7290_at",
        "51003_at",
        "3832_at",
        "51569_at",
        "80010_at",
        "55824_at",
        "7095_at",
        "10190_at",
        "11240_at",
        "6583_at",
        "6599_at",
        "8567_at",
        "85437_at",
        "6418_at",
        "9236_at",
        "55303_at",
        "26012_at",
        "2352_at",
        "7748_at",
        "144455_at",
        "8192_at",
        "5725_at",
        "5297_at",
        "79038_at",
        "9834_at",
        "11253_at",
        "55790_at",
        "64411_at",
        "23241_at",
        "389337_at",
        "966_at",
        "84869_at",
        "420_at",
        "84280_at",
        "9582_at",
        "3757_at",
        "9829_at",
        "55017_at",
        "284996_at",
        "23456_at",
        "2017_at",
        "51506_at",
        "891_at",
        "2879_at",
        "9958_at",
        "91461_at",
        "84266_at",
        "79269_at",
        "9895_at",
        "26996_at",
        "641_at",
        "7171_at",
        "5873_at",
        "9618_at",
        "4863_at",
        "152217_at",
        "79968_at",
        "11126_at",
        "57650_at",
        "1534_at",
        "23601_at",
        "284001_at",
        "6240_at",
        "8831_at",
        "26577_at",
        "9276_at",
        "388507_at",
        "4134_at",
        "6950_at",
        "1968_at",
        "57633_at",
        "5475_at",
        "3860_at",
        "10430_at",
        "57693_at",
        "90693_at",
        "158228_at",
        "55388_at",
        "55611_at",
        "29801_at",
        "339487_at",
        "60491_at",
        "286_at",
        "91662_at",
        "7464_at",
        "29095_at",
        "221830_at",
        "51282_at",
        "1186_at",
        "90273_at",
        "8225_at",
        "2993_at",
        "55186_at",
        "151246_at",
        "3203_at",
        "23317_at",
        "64066_at",
        "55247_at",
        "2994_at",
        "64216_at",
        "1894_at",
        "85462_at",
        "64215_at",
        "57189_at",
        "51318_at",
        "23095_at",
        "57498_at",
        "8825_at",
        "85236_at",
        "7168_at",
        "64207_at",
        "84166_at",
        "50515_at",
        "10049_at",
        "8623_at",
        "54491_at",
        "57217_at",
        "128061_at",
        "85451_at",
        "283635_at",
        "4709_at",
        "8867_at",
        "65005_at",
        "2237_at",
        "246243_at",
        "1317_at",
        "10361_at",
        "3563_at",
        "84302_at",
        "3145_at",
        "10125_at",
        "975_at",
        "653121_at",
        "8851_at",
        "991_at",
        "10522_at",
        "51715_at",
        "241_at",
        "23031_at",
        "83695_at",
        "11107_at",
        "9724_at",
        "81537_at",
        "65998_at",
        "80025_at",
        "1845_at",
        "5148_at",
        "56270_at",
        "23224_at",
        "8237_at",
        "114614_at",
        "23423_at",
        "51527_at",
        "4057_at",
        "79856_at",
        "140461_at",
        "200424_at",
        "100093630_at",
        "51203_at",
        "112479_at",
        "9266_at",
        "9380_at",
        "91304_at",
        "538_at",
        "6005_at",
        "84230_at",
        "23326_at",
        "2996_at",
        "100507111_at",
        "10100_at",
        "79037_at",
        "11004_at",
        "24137_at",
        "51735_at",
        "64097_at",
        "85379_at",
        "89890_at",
        "65981_at",
        "25816_at",
        "202243_at",
        "965_at",
        "9837_at",
        "57122_at",
        "6286_at",
        "119_at",
        "400793_at",
        "7389_at",
        "64776_at",
        "10120_at",
        "1379_at",
        "6122_at",
        "84270_at",
        "84206_at",
        "7272_at",
        "4751_at",
        "6006_at",
        "6146_at",
        "113402_at",
        "9055_at",
        "284_at",
        "3554_at",
        "57109_at",
        "1893_at",
        "84364_at",
        "116369_at",
        "4363_at",
        "79774_at",
        "5983_at",
        "23240_at",
        "83990_at",
        "157313_at",
        "338811_at",
        "84722_at",
        "50861_at",
        "80022_at",
        "51514_at",
        "340061_at",
        "23500_at",
        "5273_at",
        "4194_at",
        "22883_at",
        "4659_at",
        "3592_at",
        "348235_at",
        "11193_at",
        "57126_at",
        "66008_at",
        "4756_at",
        "831_at",
        "57082_at",
        "59307_at",
        "441951_at",
        "81602_at",
        "220042_at",
        "2268_at",
        "10661_at",
        "64801_at",
        "23028_at",
        "3833_at",
        "1676_at",
        "79366_at",
        "79670_at",
        "57088_at",
        "286053_at",
        "81611_at",
        "9804_at",
        "79872_at",
        "81610_at",
        "6007_at",
        "51193_at",
        "10758_at",
        "11177_at",
        "10409_at",
        "57150_at",
        "29107_at",
        "9057_at",
        "26524_at",
        "54331_at",
        "151176_at",
        "56957_at",
        "466_at",
        "9928_at",
        "8260_at",
        "51010_at",
        "1789_at",
        "5356_at",
        "113251_at",
        "7174_at",
        "644_at",
        "51447_at",
        "56172_at",
        "11157_at",
        "64743_at",
        "26099_at",
        "56905_at",
        "596_at",
        "222642_at",
        "100505792_at",
        "5552_at",
        "6651_at",
        "84250_at",
        "387521_at",
        "9156_at",
        "899_at",
        "116843_at",
        "26226_at",
        "3003_at",
        "79088_at",
        "8395_at",
        "8291_at",
        "80824_at",
        "10491_at",
        "222236_at",
        "10592_at",
        "6282_at",
        "128338_at",
        "81928_at",
        "9132_at",
        "54902_at",
        "3202_at",
        "10062_at",
        "7035_at",
        "9994_at",
        "10320_at",
        "5567_at",
        "5594_at",
        "7088_at",
        "50488_at",
        "7422_at",
        "55166_at",
        "7468_at",
        "10632_at",
        "9554_at",
        "10906_at",
        "86_at",
        "84899_at",
        "9324_at",
        "1033_at",
        "26043_at",
        "4123_at",
        "81627_at",
        "23327_at",
        "10615_at",
        "29090_at",
        "55356_at",
        "124540_at",
        "9205_at",
        "92667_at",
        "51162_at",
        "10084_at",
        "1_at",
        "2549_at",
        "388796_at",
        "84327_at",
        "51292_at",
        "258010_at",
        "56890_at",
        "284029_at",
        "23390_at",
        "151473_at",
        "11065_at",
        "100507507_at",
        "1070_at",
        "4673_at",
        "55703_at",
        "8930_at",
        "54928_at",
        "326624_at",
        "84264_at",
        "84548_at",
        "10627_at",
        "1669_at",
        "64651_at",
        "3265_at",
        "10233_at",
        "5754_at",
        "51465_at",
        "196_at",
        "64847_at",
        "100533182_at",
        "56997_at",
        "158747_at",
        "23001_at",
        "57823_at",
        "662_at",
        "7846_at",
        "158586_at",
        "79874_at",
        "54969_at",
        "10282_at",
        "26271_at",
        "55071_at",
        "80315_at",
        "3423_at",
        "10721_at",
        "91703_at",
        "9185_at",
        "23305_at",
        "54800_at",
        "167227_at",
        "7392_at",
        "64940_at",
        "55355_at",
        "10884_at",
        "2523_at",
        "57690_at",
        "481_at",
        "932_at",
        "6626_at",
        "10983_at",
        "896_at",
        "7145_at",
        "2962_at",
        "90313_at",
        "25953_at",
        "671_at",
        "50856_at",
        "54619_at",
        "81606_at",
        "55661_at",
        "51277_at",
        "4054_at",
        "22995_at",
        "3692_at",
        "55363_at",
        "79834_at",
        "259230_at",
        "2181_at",
        "5213_at",
        "4636_at",
        "163051_at",
        "995_at",
        "114991_at",
        "239_at",
        "114625_at",
        "2177_at",
        "5357_at",
        "9836_at",
        "79039_at",
        "1378_at",
        "6119_at",
        "128989_at",
        "4665_at",
        "55252_at",
        "3101_at",
        "80781_at",
        "23002_at",
        "9306_at",
        "2005_at",
        "7318_at",
        "2178_at",
        "51105_at",
        "25_at",
        "7372_at",
        "55248_at",
        "100505501_at",
        "728489_at",
        "84848_at",
        "146225_at",
        "7695_at",
        "10585_at",
        "30817_at",
        "57326_at",
        "55423_at",
        "55676_at",
        "3480_at",
        "10092_at",
        "9329_at",
        "6252_at",
        "4779_at",
        "10746_at",
        "5187_at",
        "3560_at",
        "9793_at",
        "6767_at",
        "6100_at",
        "54464_at",
        "3001_at",
        "27_at",
        "7075_at",
        "7975_at",
        "118472_at",
        "4594_at",
        "998_at",
        "56998_at",
        "8667_at",
        "3215_at",
        "9647_at",
        "4292_at",
        "1241_at",
        "3276_at",
        "4209_at",
        "2623_at",
        "29915_at",
        "4835_at",
        "645784_at",
        "79862_at",
        "9188_at",
        "9263_at",
        "3267_at",
        "51114_at",
        "5939_at",
        "11320_at",
        "115548_at",
        "54503_at",
        "83999_at",
        "84803_at",
        "51719_at",
        "317_at",
        "6710_at",
        "80851_at",
        "7855_at",
        "152195_at",
        "56948_at",
        "9584_at",
        "100499177_at",
        "54438_at",
        "9019_at",
        "57597_at",
        "5509_at",
        "6731_at",
        "51023_at",
        "6137_at",
        "387357_at",
        "10053_at",
        "10487_at",
        "27348_at",
        "79908_at",
        "55182_at",
        "6310_at",
        "92922_at",
        "4792_at"
      ],
      "rows": 202,
      "table": true,
      "tojson": true
    },
    {
      "name": "eigengenes33",
      "title": "Eigengenes of 33 modules",
      "object": "eigengenes33",
      "file": "eigengenes33.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "mds",
      "title": "MDS gene expression profile",
      "object": "mds",
      "file": "mds.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "7180_at",
        "272_at",
        "2769_at",
        "4267_at",
        "79183_at",
        "25801_at",
        "23345_at",
        "10562_at",
        "11221_at",
        "154664_at",
        "10321_at",
        "10625_at",
        "2745_at",
        "23564_at",
        "118932_at",
        "660_at",
        "634_at",
        "4973_at",
        "5004_at",
        "55062_at",
        "6645_at",
        "29094_at",
        "8555_at",
        "820_at",
        "2322_at",
        "51441_at",
        "4350_at",
        "762_at",
        "89797_at",
        "6659_at",
        "4318_at",
        "29952_at",
        "54682_at",
        "84255_at",
        "51734_at",
        "440603_at",
        "1053_at",
        "9334_at",
        "9914_at",
        "7798_at",
        "23569_at",
        "144423_at",
        "2730_at",
        "5005_at",
        "414918_at",
        "1308_at",
        "7461_at",
        "3579_at",
        "57820_at",
        "2746_at",
        "3930_at",
        "64101_at",
        "1915_at",
        "3240_at",
        "8807_at",
        "3934_at",
        "999_at",
        "23401_at",
        "50807_at",
        "2356_at",
        "170463_at",
        "91252_at",
        "1183_at",
        "9440_at",
        "84641_at",
        "440104_at",
        "8445_at",
        "343990_at",
        "1116_at",
        "22906_at",
        "353189_at",
        "163882_at",
        "63910_at",
        "8993_at",
        "123920_at",
        "23046_at",
        "7277_at",
        "550643_at",
        "5318_at",
        "100506696_at",
        "6732_at",
        "64760_at",
        "1635_at",
        "6790_at",
        "51082_at",
        "84326_at",
        "120892_at",
        "29127_at",
        "266747_at",
        "7033_at",
        "84418_at",
        "85021_at",
        "960_at",
        "80853_at",
        "5214_at",
        "3728_at",
        "8778_at",
        "126917_at",
        "57787_at",
        "861_at",
        "80196_at",
        "79689_at",
        "84078_at",
        "25797_at",
        "285958_at",
        "26034_at",
        "306_at",
        "240_at",
        "55529_at",
        "5208_at",
        "150372_at",
        "3708_at",
        "79143_at",
        "4774_at",
        "1955_at",
        "9112_at",
        "65220_at",
        "5867_at",
        "26086_at",
        "100505481_at",
        "6809_at",
        "150726_at",
        "83478_at",
        "114971_at",
        "338339_at",
        "51361_at",
        "10284_at",
        "825_at",
        "65986_at",
        "11186_at",
        "84941_at",
        "55825_at",
        "10096_at",
        "129642_at",
        "983_at",
        "7443_at",
        "9848_at",
        "58484_at",
        "5495_at",
        "23604_at",
        "90850_at",
        "1454_at",
        "6919_at",
        "55605_at",
        "56965_at",
        "3678_at",
        "81855_at",
        "253018_at",
        "79971_at",
        "55553_at",
        "89874_at",
        "4070_at",
        "9741_at",
        "51477_at",
        "10154_at",
        "148534_at",
        "8895_at",
        "63939_at",
        "9922_at",
        "4628_at",
        "1084_at",
        "9987_at",
        "3727_at",
        "6729_at",
        "317671_at",
        "2057_at",
        "10970_at",
        "54946_at",
        "1536_at",
        "4288_at",
        "2040_at",
        "388341_at",
        "23261_at",
        "55621_at",
        "159_at",
        "3425_at",
        "2531_at",
        "6624_at",
        "1432_at",
        "199675_at",
        "383_at",
        "83986_at",
        "112950_at",
        "92912_at",
        "4680_at",
        "55635_at",
        "29890_at",
        "85027_at",
        "10608_at",
        "2230_at",
        "203328_at",
        "57666_at",
        "54443_at",
        "160760_at",
        "64400_at",
        "201799_at",
        "6840_at",
        "115350_at",
        "1058_at",
        "54941_at",
        "116362_at",
        "27245_at",
        "2067_at",
        "80331_at",
        "3087_at",
        "4332_at",
        "8407_at",
        "649_at",
        "6300_at",
        "5795_at",
        "49854_at",
        "100141515_at",
        "64386_at",
        "8972_at",
        "8897_at",
        "100506548_at",
        "10565_at",
        "6590_at",
        "2648_at",
        "10945_at",
        "29997_at",
        "996_at",
        "84275_at",
        "54830_at",
        "7702_at",
        "2762_at",
        "9764_at",
        "23549_at",
        "5562_at",
        "87_at",
        "196051_at",
        "60481_at",
        "54849_at",
        "51545_at",
        "8794_at",
        "50854_at",
        "5366_at",
        "1118_at",
        "2681_at",
        "26268_at",
        "688_at",
        "56265_at",
        "81027_at",
        "23654_at",
        "2215_at",
        "30061_at",
        "1371_at",
        "51379_at",
        "9655_at",
        "9926_at",
        "8476_at",
        "140465_at",
        "83461_at",
        "100_at",
        "100129460_at",
        "6484_at",
        "56931_at",
        "5819_at",
        "978_at",
        "10335_at",
        "10890_at",
        "1759_at",
        "83540_at",
        "2258_at",
        "26018_at",
        "5359_at",
        "129080_at",
        "9949_at",
        "3772_at",
        "121512_at",
        "64858_at",
        "64151_at",
        "2357_at",
        "259266_at",
        "701_at",
        "415116_at",
        "53346_at",
        "7750_at",
        "80896_at",
        "6158_at",
        "92906_at",
        "146857_at",
        "64754_at",
        "2114_at",
        "26191_at",
        "64078_at",
        "81619_at",
        "54850_at",
        "5313_at",
        "2153_at",
        "151556_at",
        "55194_at",
        "4311_at",
        "949_at",
        "51542_at",
        "57136_at",
        "57222_at",
        "22901_at",
        "91298_at",
        "2747_at",
        "6886_at",
        "3021_at",
        "7490_at",
        "163033_at",
        "10874_at",
        "203100_at",
        "390916_at",
        "59349_at",
        "56180_at",
        "10112_at",
        "91419_at",
        "3338_at",
        "2358_at",
        "2992_at",
        "57473_at",
        "63027_at",
        "51479_at",
        "7071_at",
        "90417_at",
        "8987_at",
        "178_at",
        "113263_at",
        "55700_at",
        "6947_at",
        "2593_at",
        "166_at",
        "256691_at",
        "6283_at",
        "738_at",
        "196385_at",
        "8218_at",
        "25852_at",
        "10116_at",
        "84986_at",
        "10804_at",
        "1062_at",
        "122769_at",
        "3482_at",
        "51099_at",
        "6576_at",
        "4048_at",
        "55872_at",
        "127687_at",
        "149951_at",
        "7068_at",
        "79887_at",
        "10362_at",
        "56977_at",
        "9562_at",
        "90550_at",
        "121441_at",
        "84678_at",
        "26253_at",
        "467_at",
        "80823_at",
        "613_at",
        "23598_at",
        "408_at",
        "53831_at",
        "6691_at",
        "260429_at",
        "23061_at",
        "56992_at",
        "7709_at",
        "5087_at",
        "123096_at",
        "8575_at",
        "60314_at",
        "1938_at",
        "57106_at",
        "8030_at",
        "22824_at",
        "51523_at",
        "79733_at",
        "55350_at",
        "819_at",
        "23492_at",
        "23243_at",
        "11338_at",
        "388272_at",
        "79674_at",
        "9379_at",
        "699_at",
        "3200_at",
        "55196_at",
        "79023_at",
        "8529_at",
        "3204_at",
        "10953_at",
        "26156_at",
        "7357_at",
        "7414_at",
        "51022_at",
        "25875_at",
        "10403_at",
        "221477_at",
        "23157_at",
        "1063_at",
        "953_at",
        "51275_at",
        "5900_at",
        "284904_at",
        "56729_at",
        "29028_at",
        "441150_at",
        "4794_at",
        "91748_at",
        "11031_at",
        "54726_at",
        "3684_at",
        "7153_at",
        "339287_at",
        "10217_at",
        "84973_at",
        "55048_at",
        "29968_at",
        "54963_at",
        "3161_at",
        "541565_at",
        "93624_at",
        "3577_at",
        "5110_at",
        "8560_at",
        "25870_at",
        "84248_at",
        "353116_at",
        "5037_at",
        "5600_at",
        "8767_at",
        "1153_at",
        "4317_at",
        "6241_at",
        "890_at",
        "164312_at",
        "84162_at",
        "22913_at",
        "375190_at",
        "11072_at",
        "28987_at",
        "210_at",
        "153830_at",
        "150468_at",
        "401577_at",
        "1088_at",
        "6708_at",
        "342892_at",
        "7812_at",
        "1316_at",
        "10107_at",
        "23228_at",
        "494143_at",
        "8349_at",
        "2077_at",
        "51611_at",
        "140803_at",
        "53829_at",
        "55702_at",
        "51177_at",
        "84267_at",
        "23764_at",
        "359948_at",
        "29089_at",
        "55789_at",
        "10827_at",
        "7130_at",
        "9700_at",
        "55466_at",
        "100505573_at",
        "6877_at",
        "170394_at",
        "151162_at",
        "60436_at",
        "27436_at",
        "55215_at",
        "5427_at",
        "80758_at",
        "8666_at",
        "54973_at",
        "8875_at",
        "9787_at",
        "10844_at",
        "84188_at",
        "353_at",
        "114915_at",
        "51078_at",
        "55711_at",
        "10762_at",
        "9978_at",
        "7290_at",
        "51003_at",
        "3832_at",
        "51569_at",
        "80010_at",
        "55824_at",
        "7095_at",
        "10190_at",
        "11240_at",
        "6583_at",
        "6599_at",
        "8567_at",
        "85437_at",
        "6418_at",
        "9236_at",
        "55303_at",
        "26012_at",
        "2352_at",
        "7748_at",
        "144455_at",
        "8192_at",
        "5725_at",
        "5297_at",
        "79038_at",
        "9834_at",
        "11253_at",
        "55790_at",
        "64411_at",
        "23241_at",
        "389337_at",
        "966_at",
        "84869_at",
        "420_at",
        "84280_at",
        "9582_at",
        "3757_at",
        "9829_at",
        "55017_at",
        "284996_at",
        "23456_at",
        "2017_at",
        "51506_at",
        "891_at",
        "2879_at",
        "9958_at",
        "91461_at",
        "84266_at",
        "79269_at",
        "9895_at",
        "26996_at",
        "641_at",
        "7171_at",
        "5873_at",
        "9618_at",
        "4863_at",
        "152217_at",
        "79968_at",
        "11126_at",
        "57650_at",
        "1534_at",
        "23601_at",
        "284001_at",
        "6240_at",
        "8831_at",
        "26577_at",
        "9276_at",
        "388507_at",
        "4134_at",
        "6950_at",
        "1968_at",
        "57633_at",
        "5475_at",
        "3860_at",
        "10430_at",
        "57693_at",
        "90693_at",
        "158228_at",
        "55388_at",
        "55611_at",
        "29801_at",
        "339487_at",
        "60491_at",
        "286_at",
        "91662_at",
        "7464_at",
        "29095_at",
        "221830_at",
        "51282_at",
        "1186_at",
        "90273_at",
        "8225_at",
        "2993_at",
        "55186_at",
        "151246_at",
        "3203_at",
        "23317_at",
        "64066_at",
        "55247_at",
        "2994_at",
        "64216_at",
        "1894_at",
        "85462_at",
        "64215_at",
        "57189_at",
        "51318_at",
        "23095_at",
        "57498_at",
        "8825_at",
        "85236_at",
        "7168_at",
        "64207_at",
        "84166_at",
        "50515_at",
        "10049_at",
        "8623_at",
        "54491_at",
        "57217_at",
        "128061_at",
        "85451_at",
        "283635_at",
        "4709_at",
        "8867_at",
        "65005_at",
        "2237_at",
        "246243_at",
        "1317_at",
        "10361_at",
        "3563_at",
        "84302_at",
        "3145_at",
        "10125_at",
        "975_at",
        "653121_at",
        "8851_at",
        "991_at",
        "10522_at",
        "51715_at",
        "241_at",
        "23031_at",
        "83695_at",
        "11107_at",
        "9724_at",
        "81537_at",
        "65998_at",
        "80025_at",
        "1845_at",
        "5148_at",
        "56270_at",
        "23224_at",
        "8237_at",
        "114614_at",
        "23423_at",
        "51527_at",
        "4057_at",
        "79856_at",
        "140461_at",
        "200424_at",
        "100093630_at",
        "51203_at",
        "112479_at",
        "9266_at",
        "9380_at",
        "91304_at",
        "538_at",
        "6005_at",
        "84230_at",
        "23326_at",
        "2996_at",
        "100507111_at",
        "10100_at",
        "79037_at",
        "11004_at",
        "24137_at",
        "51735_at",
        "64097_at",
        "85379_at",
        "89890_at",
        "65981_at",
        "25816_at",
        "202243_at",
        "965_at",
        "9837_at",
        "57122_at",
        "6286_at",
        "119_at",
        "400793_at",
        "7389_at",
        "64776_at",
        "10120_at",
        "1379_at",
        "6122_at",
        "84270_at",
        "84206_at",
        "7272_at",
        "4751_at",
        "6006_at",
        "6146_at",
        "113402_at",
        "9055_at",
        "284_at",
        "3554_at",
        "57109_at",
        "1893_at",
        "84364_at",
        "116369_at",
        "4363_at",
        "79774_at",
        "5983_at",
        "23240_at",
        "83990_at",
        "157313_at",
        "338811_at",
        "84722_at",
        "50861_at",
        "80022_at",
        "51514_at",
        "340061_at",
        "23500_at",
        "5273_at",
        "4194_at",
        "22883_at",
        "4659_at",
        "3592_at",
        "348235_at",
        "11193_at",
        "57126_at",
        "66008_at",
        "4756_at",
        "831_at",
        "57082_at",
        "59307_at",
        "441951_at",
        "81602_at",
        "220042_at",
        "2268_at",
        "10661_at",
        "64801_at",
        "23028_at",
        "3833_at",
        "1676_at",
        "79366_at",
        "79670_at",
        "57088_at",
        "286053_at",
        "81611_at",
        "9804_at",
        "79872_at",
        "81610_at",
        "6007_at",
        "51193_at",
        "10758_at",
        "11177_at",
        "10409_at",
        "57150_at",
        "29107_at",
        "9057_at",
        "26524_at",
        "54331_at",
        "151176_at",
        "56957_at",
        "466_at",
        "9928_at",
        "8260_at",
        "51010_at",
        "1789_at",
        "5356_at",
        "113251_at",
        "7174_at",
        "644_at",
        "51447_at",
        "56172_at",
        "11157_at",
        "64743_at",
        "26099_at",
        "56905_at",
        "596_at",
        "222642_at",
        "100505792_at",
        "5552_at",
        "6651_at",
        "84250_at",
        "387521_at",
        "9156_at",
        "899_at",
        "116843_at",
        "26226_at",
        "3003_at",
        "79088_at",
        "8395_at",
        "8291_at",
        "80824_at",
        "10491_at",
        "222236_at",
        "10592_at",
        "6282_at",
        "128338_at",
        "81928_at",
        "9132_at",
        "54902_at",
        "3202_at",
        "10062_at",
        "7035_at",
        "9994_at",
        "10320_at",
        "5567_at",
        "5594_at",
        "7088_at",
        "50488_at",
        "7422_at",
        "55166_at",
        "7468_at",
        "10632_at",
        "9554_at",
        "10906_at",
        "86_at",
        "84899_at",
        "9324_at",
        "1033_at",
        "26043_at",
        "4123_at",
        "81627_at",
        "23327_at",
        "10615_at",
        "29090_at",
        "55356_at",
        "124540_at",
        "9205_at",
        "92667_at",
        "51162_at",
        "10084_at",
        "1_at",
        "2549_at",
        "388796_at",
        "84327_at",
        "51292_at",
        "258010_at",
        "56890_at",
        "284029_at",
        "23390_at",
        "151473_at",
        "11065_at",
        "100507507_at",
        "1070_at",
        "4673_at",
        "55703_at",
        "8930_at",
        "54928_at",
        "326624_at",
        "84264_at",
        "84548_at",
        "10627_at",
        "1669_at",
        "64651_at",
        "3265_at",
        "10233_at",
        "5754_at",
        "51465_at",
        "196_at",
        "64847_at",
        "100533182_at",
        "56997_at",
        "158747_at",
        "23001_at",
        "57823_at",
        "662_at",
        "7846_at",
        "158586_at",
        "79874_at",
        "54969_at",
        "10282_at",
        "26271_at",
        "55071_at",
        "80315_at",
        "3423_at",
        "10721_at",
        "91703_at",
        "9185_at",
        "23305_at",
        "54800_at",
        "167227_at",
        "7392_at",
        "64940_at",
        "55355_at",
        "10884_at",
        "2523_at",
        "57690_at",
        "481_at",
        "932_at",
        "6626_at",
        "10983_at",
        "896_at",
        "7145_at",
        "2962_at",
        "90313_at",
        "25953_at",
        "671_at",
        "50856_at",
        "54619_at",
        "81606_at",
        "55661_at",
        "51277_at",
        "4054_at",
        "22995_at",
        "3692_at",
        "55363_at",
        "79834_at",
        "259230_at",
        "2181_at",
        "5213_at",
        "4636_at",
        "163051_at",
        "995_at",
        "114991_at",
        "239_at",
        "114625_at",
        "2177_at",
        "5357_at",
        "9836_at",
        "79039_at",
        "1378_at",
        "6119_at",
        "128989_at",
        "4665_at",
        "55252_at",
        "3101_at",
        "80781_at",
        "23002_at",
        "9306_at",
        "2005_at",
        "7318_at",
        "2178_at",
        "51105_at",
        "25_at",
        "7372_at",
        "55248_at",
        "100505501_at",
        "728489_at",
        "84848_at",
        "146225_at",
        "7695_at",
        "10585_at",
        "30817_at",
        "57326_at",
        "55423_at",
        "55676_at",
        "3480_at",
        "10092_at",
        "9329_at",
        "6252_at",
        "4779_at",
        "10746_at",
        "5187_at",
        "3560_at",
        "9793_at",
        "6767_at",
        "6100_at",
        "54464_at",
        "3001_at",
        "27_at",
        "7075_at",
        "7975_at",
        "118472_at",
        "4594_at",
        "998_at",
        "56998_at",
        "8667_at",
        "3215_at",
        "9647_at",
        "4292_at",
        "1241_at",
        "3276_at",
        "4209_at",
        "2623_at",
        "29915_at",
        "4835_at",
        "645784_at",
        "79862_at",
        "9188_at",
        "9263_at",
        "3267_at",
        "51114_at",
        "5939_at",
        "11320_at",
        "115548_at",
        "54503_at",
        "83999_at",
        "84803_at",
        "51719_at",
        "317_at",
        "6710_at",
        "80851_at",
        "7855_at",
        "152195_at",
        "56948_at",
        "9584_at",
        "100499177_at",
        "54438_at",
        "9019_at",
        "57597_at",
        "5509_at",
        "6731_at",
        "51023_at",
        "6137_at",
        "387357_at",
        "10053_at",
        "10487_at",
        "27348_at",
        "79908_at",
        "55182_at",
        "6310_at",
        "92922_at",
        "4792_at"
      ],
      "rows": 164,
      "table": true,
      "tojson": true
    },
    {
      "name": "pigengene",
      "title": "An object of class 'Pigengene'",
      "object": "pigengene",
      "file": "pigengene.RData",
      "class": [
        "pigengene"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "Pigengene-package",
      "title": "Infers robust biological signatures from gene expression data",
      "topics": [
        "Pigengene-package",
        "Pigengene"
      ]
    },
    {
      "page": "aml",
      "title": "AML gene expression profile",
      "topics": [
        "aml"
      ]
    },
    {
      "page": "apply.filter",
      "title": "Applies a given filter on the data",
      "topics": [
        "apply.filter"
      ]
    },
    {
      "page": "balance",
      "title": "Balances the number of samples",
      "topics": [
        "balance"
      ]
    },
    {
      "page": "calculate.beta",
      "title": "Estimates an appropriate power value",
      "topics": [
        "calculate.beta"
      ]
    },
    {
      "page": "check.nas",
      "title": "Removes 'NA's from a data matrix",
      "topics": [
        "check.nas"
      ]
    },
    {
      "page": "check.pigengene.input",
      "title": "Quality check on the imput",
      "topics": [
        "check.pigengene.input"
      ]
    },
    {
      "page": "combine.networks",
      "title": "Combines two or more networks",
      "topics": [
        "combine.networks"
      ]
    },
    {
      "page": "compact.tree",
      "title": "Reduces the number of genes in a decision tree",
      "topics": [
        "compact.tree"
      ]
    },
    {
      "page": "compute.pigengene",
      "title": "Computes the eigengenes",
      "topics": [
        "compute.pigengene"
      ]
    },
    {
      "page": "dcor.matrix",
      "title": "Computes distance correlation for give matrix",
      "topics": [
        "dcor.matrix"
      ]
    },
    {
      "page": "determine.modules",
      "title": "Identifies modules of the network",
      "topics": [
        "determine.modules"
      ]
    },
    {
      "page": "draw.bn",
      "title": "Draws a Bayesian network",
      "topics": [
        "draw.bn"
      ]
    },
    {
      "page": "eigengenes33",
      "title": "Eigengenes of 33 modules",
      "topics": [
        "eigengenes33"
      ]
    },
    {
      "page": "gene.mapping",
      "title": "Maps gene IDs",
      "topics": [
        "gene.mapping"
      ]
    },
    {
      "page": "get.enriched.pw",
      "title": "Performs pathway over representation analysis",
      "topics": [
        "get.enriched.pw"
      ]
    },
    {
      "page": "get.fitted.leaf",
      "title": "Returs the leaf for each sample",
      "topics": [
        "get.fitted.leaf"
      ]
    },
    {
      "page": "get.genes",
      "title": "List the (most relevant) genes for a decision tree.",
      "topics": [
        "get.genes"
      ]
    },
    {
      "page": "get.used.features",
      "title": "Return the features used in a tree",
      "topics": [
        "get.used.features"
      ]
    },
    {
      "page": "learn.bn",
      "title": "Learns a Bayesian network",
      "topics": [
        "learn.bn"
      ]
    },
    {
      "page": "make.decision.tree",
      "title": "Creates a decision tree to classify samples using the eigengenes values",
      "topics": [
        "make.decision.tree"
      ]
    },
    {
      "page": "make.filter",
      "title": "Computes the filter based on a similarity network",
      "topics": [
        "make.filter"
      ]
    },
    {
      "page": "mds",
      "title": "MDS gene expression profile",
      "topics": [
        "mds"
      ]
    },
    {
      "page": "message.if",
      "title": "Conditional messaging.",
      "topics": [
        "message.if"
      ]
    },
    {
      "page": "module.heatmap",
      "title": "Plots heatmaps for modules",
      "topics": [
        "module.heatmap"
      ]
    },
    {
      "page": "one.step.pigengene",
      "title": "Runs the entire Pigengene pipeline",
      "topics": [
        "one.step.pigengene"
      ]
    },
    {
      "page": "pheatmap.type",
      "title": "Plots heatmap with clustering only within types.",
      "topics": [
        "pheatmap.type"
      ]
    },
    {
      "page": "pigengene",
      "title": "An object of class 'Pigengene'",
      "topics": [
        "pigengene"
      ]
    },
    {
      "page": "pigengene-class",
      "title": "The pigengene class",
      "topics": [
        "pigengene-class",
        "plot, pigengene-method"
      ]
    },
    {
      "page": "plot.pigengene",
      "title": "Plots and saves a 'pigengene' object",
      "topics": [
        "plot.pigengene"
      ]
    },
    {
      "page": "preds.at",
      "title": "Prediction using a possibly compacted tree",
      "topics": [
        "preds.at"
      ]
    },
    {
      "page": "project.eigen",
      "title": "Infers eigengenes for given expression data",
      "topics": [
        "project.eigen"
      ]
    },
    {
      "page": "pvalues.manova",
      "title": "Computes pvalues for multi-class differential expression",
      "topics": [
        "pvalues.manova"
      ]
    },
    {
      "page": "save.if",
      "title": "Saves an object verbosely.",
      "topics": [
        "save.if"
      ]
    },
    {
      "page": "wgcna.one.step",
      "title": "Module identification",
      "topics": [
        "wgcna.one.step"
      ]
    }
  ],
  "_rundeps": [
    "aisdk",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "backports",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "BiocStyle",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bnlearn",
    "bookdown",
    "bslib",
    "C50",
    "cachem",
    "callr",
    "checkmate",
    "cli",
    "cluster",
    "clusterProfiler",
    "codetools",
    "colorspace",
    "cpp11",
    "crayon",
    "Cubist",
    "curl",
    "data.table",
    "DBI",
    "digest",
    "dir.expiry",
    "doParallel",
    "DOSE",
    "dplyr",
    "dynamicTreeCut",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastcluster",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "gdata",
    "gdtools",
    "generics",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggraph",
    "ggrepel",
    "ggtangle",
    "ggtree",
    "glue",
    "GO.db",
    "GOSemSim",
    "graph",
    "graphite",
    "graphlayouts",
    "gridExtra",
    "gridGraphics",
    "gson",
    "gtable",
    "gtools",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "impute",
    "inum",
    "IRanges",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "lattice",
    "lazyeval",
    "libcoin",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "memoise",
    "mime",
    "mvtnorm",
    "nlme",
    "nnet",
    "openssl",
    "openxlsx",
    "partykit",
    "patchwork",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "preprocessCore",
    "processx",
    "ps",
    "purrr",
    "qvalue",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reactome.db",
    "ReactomePA",
    "reshape2",
    "Rgraphviz",
    "rlang",
    "rmarkdown",
    "rpart",
    "RSQLite",
    "rstudioapi",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterpie",
    "Seqinfo",
    "stringi",
    "stringr",
    "survival",
    "sys",
    "systemfonts",
    "tibble",
    "tidydr",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tidytree",
    "tinytex",
    "treeio",
    "tweenr",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "WGCNA",
    "withr",
    "xfun",
    "XVector",
    "yaml",
    "yulab.utils",
    "zip"
  ],
  "_score": 3.670245853074124,
  "_indexed": true,
  "_nocasepkg": "pigengene",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-05-30T08:21:28.000Z",
      "distro": "noble",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "cb98ce2010243f7ec9b92e6913ebf0c9cd8e639cadf1756f146cdbd50ae1220f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.39.0",
      "date": "2026-05-30T08:21:50.000Z",
      "distro": "noble",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "b3353672f62a98a5d619e9a534d7458e6e6d99a4a2ce364076312c86600f77c6",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-05-30T11:50:24.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "cb777bb885aa0ebe1d2589e652d5104f0afd3c29a9a6c0d7b4e26b7ee5c4208c",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.39.0",
      "date": "2026-05-30T11:49:51.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "3a103912c1d401d1e502c234dc74b7b5745548bc4b74f56f18e9e52d83331ced",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.39.0",
      "date": "2026-05-30T08:21:43.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "dbb40c398ccb125baa356346af51caebcc1af863acbc3eda981f5f2e0c7961ba",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-30T08:19:30.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "1755c7d693cb9edc7ec0268fbbf32701a58c4cc6ddc13f2bb00437553b84a846",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-30T08:19:32.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "b45ede46a0ed5051bc5fa628cc1773c0cb868d76b0c2219dc97fa18170d5d043",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.39.0",
      "date": "2026-05-30T08:19:28.000Z",
      "commit": "cc08c7aba6154b530e62af509efa2f5f7afb239c",
      "fileid": "6130ae447021e13f7877bc981d2eeff6e57a41fc3905763941b482bcfa53aab3",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677910098"
    }
  ]
}