{
  "_id": "6a1f2bf4b401979e73425966",
  "Package": "oposSOM",
  "Title": "Comprehensive analysis of transcriptome data",
  "Version": "2.31.0",
  "Description": "This package translates microarray expression data into\nmetadata of reduced dimension. It provides various\nsample-centered and group-centered visualizations, sample\nsimilarity analyses and functional enrichment analyses. The\nunderlying SOM algorithm combines feature clustering,\nmultidimensional scaling and dimension reduction, along with\nstrong visualization capabilities. It enables extraction and\ndescription of functional expression modules inherent in the\ndata.",
  "License": "GPL (>=2)",
  "Author": "Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>, Hoang Thanh\nLe <le@izbi.uni-leipzig.de> and Martin Kalcher\n<mkalcher@porkbox.net>",
  "Maintainer": "Henry Loeffler-Wirth <wirth@izbi.uni-leipzig.de>",
  "URL": "http://som.izbi.uni-leipzig.de",
  "biocViews": "GeneExpression, DifferentialExpression, GeneSetEnrichment,\nDataRepresentation, Visualization",
  "Config/pak/sysreqs": "libglpk-dev make libicu-dev libpng-dev libxml2-dev\nlibssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:39:21 UTC",
  "RemoteUrl": "https://github.com/bioc/oposSOM",
  "RemoteRef": "HEAD",
  "RemoteSha": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-15 10:08:16 UTC",
    "User": "root"
  },
  "MD5sum": "dbc175f10e1ce1c188b2f77ec0875fd5",
  "_user": "bioc",
  "_type": "src",
  "_file": "oposSOM_2.31.0.tar.gz",
  "_fileid": "1d474afdff5f74eeb793ec8654e1c3154007b179278112cebbbc23761f437494",
  "_filesize": 13969120,
  "_sha256": "1d474afdff5f74eeb793ec8654e1c3154007b179278112cebbbc23761f437494",
  "_created": "2026-05-15T10:08:16.000Z",
  "_published": "2026-06-02T19:16:04.111Z",
  "_jobs": [
    {
      "job": 79152183702,
      "time": 173,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7014801347"
    },
    {
      "job": 79152184271,
      "time": 283,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7014831554"
    },
    {
      "job": 79152183737,
      "time": 350,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7014850756"
    },
    {
      "job": 79152184150,
      "time": 254,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014823279"
    },
    {
      "job": 79152183761,
      "time": 315,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014840608"
    },
    {
      "job": 79152184669,
      "time": 208,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7014848480"
    },
    {
      "job": 79152184226,
      "time": 376,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7014858596"
    },
    {
      "job": 79152183867,
      "time": 203,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014824736"
    },
    {
      "job": 79152183752,
      "time": 379,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014922163"
    },
    {
      "job": 79152183304,
      "time": 263,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014752690"
    },
    {
      "job": 79152183114,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7367488949"
    },
    {
      "job": 79152183864,
      "time": 250,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "7014822140"
    },
    {
      "job": 79152183911,
      "time": 244,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "7014821727"
    },
    {
      "job": 79152183878,
      "time": 244,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7014820263"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 4,
    "note": 15
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/oposSOM",
  "_commit": {
    "id": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
    "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": 1777379961
  },
  "_maintainer": {
    "name": "Henry Loeffler-Wirth",
    "email": "wirth@izbi.uni-leipzig.de",
    "login": "hloefflerwirth",
    "uuid": 32058202
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "igraph",
      "version": ">= 1.0.0",
      "role": "Depends"
    },
    {
      "package": "RcppParallel",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "fastICA",
      "role": "Imports"
    },
    {
      "package": "tsne",
      "role": "Imports"
    },
    {
      "package": "scatterplot3d",
      "role": "Imports"
    },
    {
      "package": "pixmap",
      "role": "Imports"
    },
    {
      "package": "fdrtool",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "biomaRt",
      "role": "Imports"
    },
    {
      "package": "Biobase",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "graph",
      "role": "Imports"
    },
    {
      "package": "XML",
      "role": "Imports"
    },
    {
      "package": "png",
      "role": "Imports"
    },
    {
      "package": "RCurl",
      "role": "Imports"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.31.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.30.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "geneexpression",
    "differentialexpression",
    "genesetenrichment",
    "datarepresentation",
    "visualization",
    "cpp"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 476,
    "source": "https://www.bioconductor.org/packages/stats/bioc/oposSOM"
  },
  "_mentions": 27,
  "_searchresults": 11,
  "_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/oposSOM.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1-1",
      "date": "2011-06-17"
    },
    {
      "version": "0.1-3",
      "date": "2011-07-27"
    },
    {
      "version": "0.1-4",
      "date": "2012-04-12"
    },
    {
      "version": "0.2-1",
      "date": "2012-06-27"
    },
    {
      "version": "0.2-2",
      "date": "2012-10-17"
    },
    {
      "version": "0.2-3",
      "date": "2013-08-13"
    }
  ],
  "_exports": [
    "_oposSOM_calculateDelta",
    "_oposSOM_calculateEuclideanDistances",
    "_oposSOM_calculateNeighborhoodMatrix",
    "_oposSOM_matrixToCodebookMatrix",
    "biomart.available",
    "calculateDelta",
    "calculateEuclideanDistances",
    "calculateNeighborhoodMatrix",
    "circle",
    "col.pix",
    "color.palette.discrete",
    "color.palette.heatmaps",
    "color.palette.interlace",
    "color.palette.portraits",
    "color.palette.portraits.cbs",
    "GeneSet.Fisher",
    "GeneSet.maxmean",
    "get.beta.statistic",
    "get.neighbors",
    "Get.Running.Average",
    "heatmap",
    "heatmap.A4",
    "matrixToCodebookMatrix",
    "modules.chromosomes",
    "modules.CSV.sheets",
    "modules.profiles",
    "modules.relations",
    "modules.report.sheets",
    "newProgressBar",
    "opossom.new",
    "opossom.run",
    "pathway.expression.mapping",
    "pipeline.affymetrixQualityCheck",
    "pipeline.cancerHallmarks",
    "pipeline.checkInputParameters",
    "pipeline.chromosomeExpressionReports",
    "pipeline.detectCorrelationModules",
    "pipeline.detectDMapModules",
    "pipeline.detectEnsemblDataset",
    "pipeline.detectGroupOverexpressionModules",
    "pipeline.detectKMeansModules",
    "pipeline.detectOverexpressionModules",
    "pipeline.detectSpotsModules",
    "pipeline.detectUnderexpressionModules",
    "pipeline.differenceAnalyses",
    "pipeline.diffExpressionStatistics",
    "pipeline.entropyProfiles",
    "pipeline.geneLists",
    "pipeline.generateSOM",
    "pipeline.genesetOverviews",
    "pipeline.genesetProfilesAndMaps",
    "pipeline.genesetStatisticModules",
    "pipeline.genesetStatisticSamples",
    "pipeline.groupAnalysis",
    "pipeline.groupAssignment",
    "pipeline.groupSpecificGenesets",
    "pipeline.htmlDifferencesSummary",
    "pipeline.htmlGenesetAnalysis",
    "pipeline.htmlGroupSummary",
    "pipeline.htmlModuleSummary",
    "pipeline.htmlPsfAnalysis",
    "pipeline.htmlSampleSummary",
    "pipeline.htmlSummary",
    "pipeline.moduleCorrelationMap",
    "pipeline.patAssignment",
    "pipeline.prepareAnnotation",
    "pipeline.prepareIndata",
    "pipeline.PSFcalculation",
    "pipeline.PSFoutput",
    "pipeline.qualityCheck",
    "pipeline.sampleExpressionPortraits",
    "pipeline.sampleSimilarityAnalysisCor",
    "pipeline.sampleSimilarityAnalysisED",
    "pipeline.sampleSimilarityAnalysisICA",
    "pipeline.sampleSimilarityAnalysisSOM",
    "pipeline.summarySheetsGroups",
    "pipeline.summarySheetsModules",
    "pipeline.summarySheetsPATs",
    "pipeline.summarySheetsSamples",
    "pipeline.supportingMaps",
    "pipeline.topologyProfiles",
    "plot.psf.pathway.keggrest",
    "plot.psf.titlepage",
    "psf.flow",
    "psf.overview.heatmaps",
    "psf.report.sheets",
    "Quantile.Normalization",
    "radarchart",
    "Sample.GSZ",
    "Smooth.Matrix",
    "som.linear.init",
    "som.linear.init.subdata",
    "som.training",
    "som.training.phase",
    "sort.label",
    "spot.borders",
    "util.call",
    "util.cat",
    "util.fatal",
    "util.info",
    "util.load",
    "util.log",
    "util.progress",
    "util.progress.terminate",
    "util.save",
    "util.warn",
    "workspace.check"
  ],
  "_datasets": [
    {
      "name": "opossom.genesets",
      "title": "Additional literature genesets",
      "object": "opossom.genesets",
      "file": "opossom.genesets.RData",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "opossom.tissues",
      "title": "Example data set.",
      "object": "opossom.tissues",
      "file": "opossom.tissues.RData",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "liver",
        "kidney cortex",
        "thyroid gland",
        "small intestine",
        "prostate",
        "tongue",
        "testis",
        "skeletal muscle",
        "bone marrow",
        "lymph node",
        "accumbens",
        "cerebral cortex"
      ],
      "rows": 20957,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "oposSOM-package",
      "title": "Comprehensive analysis of transciptome data",
      "topics": [
        "oposSOM-package",
        "oposSOM"
      ]
    },
    {
      "page": "opossom.genesets",
      "title": "Additional literature genesets",
      "topics": [
        "opossom.genesets"
      ]
    },
    {
      "page": "opossom.new",
      "title": "Initialize the oposSOM pipeline.",
      "topics": [
        "opossom.new"
      ]
    },
    {
      "page": "opossom.run",
      "title": "Execute the oposSOM pipeline.",
      "topics": [
        "opossom.run"
      ]
    },
    {
      "page": "opossom.tissues",
      "title": "Example data set.",
      "topics": [
        "opossom.tissues"
      ]
    }
  ],
  "_rundeps": [
    "AnnotationDbi",
    "ape",
    "askpass",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "dbplyr",
    "digest",
    "dplyr",
    "fastICA",
    "fastmap",
    "fdrtool",
    "filelock",
    "generics",
    "glue",
    "graph",
    "hms",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "jsonlite",
    "KEGGREST",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "nlme",
    "openssl",
    "pillar",
    "pixmap",
    "pkgconfig",
    "png",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "RcppParallel",
    "RCurl",
    "rlang",
    "RSQLite",
    "S4Vectors",
    "scatterplot3d",
    "Seqinfo",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tsne",
    "utf8",
    "vctrs",
    "withr",
    "XML",
    "xml2",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Vignette.Rnw",
      "filename": "Vignette.pdf",
      "title": "The oposSOM users guide",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2014-07-01 20:38:11",
      "modified": "2021-01-14 15:56:22",
      "commits": 8
    }
  ],
  "_score": 4.342422680822207,
  "_indexed": true,
  "_nocasepkg": "opossom",
  "_universes": [
    "bioc",
    "hloefflerwirth"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.31.0",
      "date": "2026-05-15T10:11:23.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "02415719463beacaaf5ffe593af2201b1be7e66621b09cab5d94e9592a8f16fd",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.31.0",
      "date": "2026-05-15T10:12:06.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "c478801ab7d94cbe4292a83854e89f5129e8ec062a99bbf5247c1d09bda4a10f",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.31.0",
      "date": "2026-05-15T10:11:10.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "aef3a2ae2261d5bbc2d518ca14c3f7f9eded7bf1100ccacb15c9b105779b9755",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.31.0",
      "date": "2026-05-15T10:11:51.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "ad24c10b1b4a08c54f0340953672482c5f27dec9986d75f7e8d4f93b6775c1f9",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.31.0",
      "date": "2026-05-15T10:12:45.000Z",
      "arch": "aarch64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "70b5510be9d83445866e34811ba2467a42940957d00432ff98360533a2f2a856",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.31.0",
      "date": "2026-05-15T10:11:57.000Z",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "87ec5851b156a3838730da54e03e6e4f28396b90e40fd747c33456927c5fa1ec",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.31.0",
      "date": "2026-05-15T10:11:18.000Z",
      "arch": "aarch64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "7faa02b5080a0b0c655f875e6adbb432c9169998c4faeeef4e1130deffe8d936",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.31.0",
      "date": "2026-05-15T10:16:01.000Z",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "79798d04c78fa7a9e0f52996ea45135e00cb7a6c40373a6a479f1e59fea89e49",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.31.0",
      "date": "2026-05-15T10:10:01.000Z",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "08781721f9dd3b78e22e8dff55c83bef336d581f439bfc62f4bc0c157bc60e2d",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.31.0",
      "date": "2026-05-15T10:10:16.000Z",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "6f01b168c3ef46168b1826482a88a7d949bd9aa26f1a59c2238322165fe41321",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.31.0",
      "date": "2026-05-15T10:10:04.000Z",
      "arch": "x86_64",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "ff77999ac9502201cf5b0b709d673b8fce5a1e306d1786e5ba932b1d73e145ca",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.31.0",
      "date": "2026-06-02T19:15:26.000Z",
      "arch": "emscripten",
      "commit": "bd9c5d7b1f461492597f9f1c5c66a900759f8241",
      "fileid": "a4925b3273a1634d8be27f4832234943449a0b503e83f4b874ca8a7851ab754e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25912089637"
    }
  ]
}