{ "_id": "6a1e95f91d7bb097a0a6be72", "Package": "oposSOM", "Title": "Comprehensive analysis of transcriptome data", "Version": "2.30.0", "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 , Hoang Thanh\nLe and Martin Kalcher\n", "Maintainer": "Henry Loeffler-Wirth ", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:39:21 UTC", "RemoteUrl": "https://github.com/bioc/oposSOM", "RemoteRef": "RELEASE_3_23", "RemoteSha": "2839a282689f3e83189a93bd7fdb61aff2962688", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 08:26:06 UTC", "User": "root" }, "MD5sum": "0632f0babcbed3f5739bfbf73ee65c7f", "_user": "bioc-release", "_type": "src", "_file": "oposSOM_2.30.0.tar.gz", "_fileid": "4f73091b0330323e3868490f13515ddcaf23d1b56db1d9fe77704a2485bd1a73", "_filesize": 13969791, "_sha256": "4f73091b0330323e3868490f13515ddcaf23d1b56db1d9fe77704a2485bd1a73", "_created": "2026-06-02T08:26:06.000Z", "_published": "2026-06-02T08:36:09.226Z", "_jobs": [ { "job": 79030007435, "time": 197, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7352729692" }, { "job": 79030007510, "time": 289, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7352763678" }, { "job": 79030007527, "time": 318, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7352772046" }, { "job": 79030007517, "time": 279, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7352760723" }, { "job": 79030007522, "time": 279, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7352759278" }, { "job": 79030007605, "time": 457, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7352835523" }, { "job": 79030007597, "time": 487, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7352840935" }, { "job": 79030007550, "time": 204, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7352743460" }, { "job": 79030007543, "time": 379, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7352795553" }, { "job": 79029273189, "time": 267, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7352664320" }, { "job": 79030007467, "time": 141, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7352711842" }, { "job": 79030007506, "time": 290, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7352762921" }, { "job": 79030007568, "time": 265, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7352754378" }, { "job": 79030007557, "time": 283, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7352760857" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/oposSOM", "_commit": { "id": "2839a282689f3e83189a93bd7fdb61aff2962688", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379961 }, "_maintainer": { "name": "Henry Loeffler-Wirth", "email": "wirth@izbi.uni-leipzig.de", "login": "hloefflerwirth", "description": "", "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": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_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": 480, "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": false, "_nocasepkg": "opossom", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/oposSOM", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.30.0", "date": "2026-06-02T08:29:16.000Z", "distro": "noble", "arch": "aarch64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "875ca2e9426a2beade73d2530c80dc656f9534970bea94aa7e64485eb9a26c69", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.7.0", "os": "linux", "version": "2.30.0", "date": "2026-06-02T08:29:45.000Z", "distro": "noble", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "829e422ef5dcaa747c05eb6c4f44f03d3405cd13a7465f39a1f21651454318b9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "linux", "version": "2.30.0", "date": "2026-06-02T08:29:35.000Z", "distro": "noble", "arch": "aarch64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "eb051ce884b4069eb3bb1aaee1bad2ed7c70abbceebedbe6cf231843be317206", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "linux", "version": "2.30.0", "date": "2026-06-02T08:29:26.000Z", "distro": "noble", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "2696e2a11fc49ced0bbbd88a645b2e5e4f740b79fd21ff70afa68fd6e6072dbd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.5.3", "os": "mac", "version": "2.30.0", "date": "2026-06-02T08:29:29.000Z", "arch": "aarch64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "f56a3744631bc9c968a6a2091f449792ae1362840bd3aa0056f92a4cf20e0077", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.5.3", "os": "mac", "version": "2.30.0", "date": "2026-06-02T08:31:20.000Z", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "07e075b42a883ab7d25552cf5547aba2a6508e106bc78498c68992a392a79006", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "mac", "version": "2.30.0", "date": "2026-06-02T08:28:59.000Z", "arch": "aarch64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "d3d21af042fffa60076bc828daa60f34ca8efb756ff439ec2e2048832cddeeba", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "mac", "version": "2.30.0", "date": "2026-06-02T08:29:59.000Z", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "13117d5d0383f15cc3a9a58a7ab8ec9f3c5338173b404ef393d4642b97a75d4f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "wasm", "version": "2.30.0", "date": "2026-06-02T08:29:02.000Z", "arch": "emscripten", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "9dbc5c4c644773abf92537c8c0bda6774cd52e20e7e12ec84c49dd76274d2ded", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.7.0", "os": "win", "version": "2.30.0", "date": "2026-06-02T08:27:55.000Z", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "d589d9c38c984dec1b3687f8088a4712788cb39f761dc88b175a7ac5a4f48f9c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.5.3", "os": "win", "version": "2.30.0", "date": "2026-06-02T08:27:56.000Z", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "3e1ce3545f4aa69e1c929d6c5d42b49c19a24804eab82f681e0082dc5485fc32", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" }, { "r": "4.6.0", "os": "win", "version": "2.30.0", "date": "2026-06-02T08:28:18.000Z", "arch": "x86_64", "commit": "2839a282689f3e83189a93bd7fdb61aff2962688", "fileid": "9a55c0bd5c1aceaed8ba4d6a8d2aaa8c026b0a9dfb1618dcf627a44585ca34a7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807662815" } ] }