{ "_id": "6a493ec7a19c9318096e7d24", "Package": "consICA", "Type": "Package", "biocViews": "Technology, StatisticalMethod, Sequencing, RNASeq,\nTranscriptomics, Classification, FeatureExtraction", "Title": "consensus Independent Component Analysis", "Version": "2.11.0", "Authors@R": "c(person(given = \"Petr V.\",\nfamily = \"Nazarov\",\nrole = c(\"aut\", \"cre\"),\nemail = \"petr.nazarov@lih.lu\",\ncomment = c(ORCID = \"0000-0003-3443-0298\")),\nperson(given = \"Tony\",\nfamily = \"Kaoma\",\nrole=\"aut\",\nemail=\"tony.kaoma@lih.lu\",\ncomment = c(ORCID = \"0000-0002-1269-4826\")),\nperson(given = \"Maryna\",\nfamily = \"Chepeleva\",\nrole = c(\"aut\"),\nemail = \"maryna.chepeleva@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3036-4916\"))\n)", "Description": "consICA implements a data-driven deconvolution method –\nconsensus independent component analysis (ICA) to decompose\nheterogeneous omics data and extract features suitable for\npatient diagnostics and prognostics. The method separates\nbiologically relevant transcriptional signals from technical\neffects and provides information about the cellular composition\nand biological processes. The implementation of parallel\ncomputing in the package ensures efficient analysis of modern\nmulticore systems.", "BugReports": "https://github.com/biomod-lih/consICA/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make libpng-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:59 UTC", "RemoteUrl": "https://github.com/bioc/consICA", "RemoteRef": "HEAD", "RemoteSha": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 03:56:16 UTC", "User": "root" }, "Author": "Petr V. Nazarov [aut, cre] (ORCID:\n),\nTony Kaoma [aut] (ORCID: ),\nMaryna Chepeleva [aut] (ORCID: )", "Maintainer": "Petr V. Nazarov ", "_user": "bioc", "_type": "src", "_file": "consICA_2.11.0.tar.gz", "_fileid": "https://r2.ropensci.org/08c09563646c50d21500e3db1062425678c228db759f198e359edccdc17ced50", "_filesize": 3584499, "_sha256": "08c09563646c50d21500e3db1062425678c228db759f198e359edccdc17ced50", "_expires": "2026-10-12T17:11:33.000Z", "_created": "2026-07-04T03:56:16.000Z", "_published": "2026-07-04T17:11:35.847Z", "_bioccheck": { "error": 0, "warning": 0, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452", "_status": "success", "_upstream": "https://github.com/bioc/consICA", "_commit": { "id": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381139 }, "_maintainer": { "name": "Petr V. Nazarov", "email": "petr.nazarov@lih.lu", "login": "biomod-lih", "description": "", "uuid": 96127595, "orcid": "0000-0003-3443-0298" }, "_distro": "resolute", "_jobs": [ { "job": 85151073198, "time": 241, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8078098330" }, { "job": 85151073211, "time": 423, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8078118763" }, { "job": 85151072966, "time": 394, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8078115585" }, { "job": 85151073063, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8078094679" }, { "job": 85151073180, "time": 263, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8078101031" }, { "job": 85151072755, "time": 367, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8078072342" }, { "job": 85151073207, "time": 236, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8078097827" }, { "job": 85151073095, "time": 365, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8078112143" }, { "job": 85151073121, "time": 379, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8078113709" }, { "job": 85151073045, "time": 354, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8078111151" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "fastICA", "version": ">= 1.2.1", "role": "Imports" }, { "package": "sm", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "GO.db", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "graph", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rfast", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "topGO", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 3 }, { "week": "2025-40", "n": 1 }, { "week": "2025-43", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.11.0", "bioc": "3.24" }, { "branch": "release", "version": "2.10.0", "bioc": "3.23" } ], "_topics": [ "technology", "statisticalmethod", "sequencing", "rnaseq", "transcriptomics", "classification", "featureextraction" ], "_stars": 0, "_contributors": [ { "user": "marynachepeleva", "count": 46, "uuid": 23363957 }, { "user": "biomod-lih", "count": 33, "uuid": 96127595 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/biomod-lih/consica", "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/consICA.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/biomod-lih/consica", "_realowner": "bioc", "_cranurl": false, "_exports": [ "anovaIC", "consICA", "estimateVarianceExplained", "getFeatures", "getGO", "is.consICA", "oneICA", "overlapGO", "plotICVarianceExplained", "saveReport", "setOrientation", "sortDataFrame", "survivalAnalysis" ], "_datasets": [ { "name": "samples_data", "title": "Samples of gene expression", "object": "samples_data", "file": "samples_data.rda", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "anovaIC", "title": "ANOVA test for independent component across factors", "topics": [ "anovaIC" ] }, { "page": "consICA", "title": "Calculate consensus Independent Component Analysis", "topics": [ "consICA" ] }, { "page": "enrichGO", "title": "Enrichment analysis of GO-terms based on Ensembl IDs", "topics": [ "enrichGO" ] }, { "page": "estimateVarianceExplained", "title": "Estimate the variance explained by the model", "topics": [ "estimateVarianceExplained" ] }, { "page": "getFeatures", "title": "Get features from consICA deconvolution result", "topics": [ "getFeatures" ] }, { "page": "getGO", "title": "Assigns IC signatures to Gene Ontologies", "topics": [ "getGO" ] }, { "page": "is.consICA", "title": "Is the object is consensus ICA compliant?", "topics": [ "is.consICA" ] }, { "page": "oneICA", "title": "Runs 'fastICA'", "topics": [ "oneICA" ] }, { "page": "overlapGO", "title": "Similarity of two gene ontologies lists", "topics": [ "overlapGO" ] }, { "page": "plotICVarianceExplained", "title": "Barplot variance explained by each IC", "topics": [ "plotICVarianceExplained" ] }, { "page": "samples_data", "title": "Samples of gene expression", "topics": [ "samples_data" ] }, { "page": "saveReport", "title": "Save PDF report with analysis of each independent component", "topics": [ "saveReport" ] }, { "page": "setOrientation", "title": "Set orientation for independent components", "topics": [ "setOrientation" ] }, { "page": "sortDataFrame", "title": "Sort dataframe", "topics": [ "sortDataFrame" ] }, { "page": "survivalAnalysis", "title": "Survival analysis based on significant IC", "topics": [ "survivalAnalysis" ] } ], "_readme": "https://github.com/bioc/consICA/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "farver", "fastICA", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "GO.db", "graph", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "org.Hs.eg.db", "pheatmap", "pkgconfig", "png", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppParallel", "Rfast", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "sm", "snow", "SparseArray", "SparseM", "SummarizedExperiment", "survival", "sys", "topGO", "vctrs", "viridisLite", "withr", "XVector", "zigg" ], "_vignettes": [ { "source": "ConsICA.Rmd", "filename": "ConsICA.html", "title": "The consICa package: User’s manual", "author": "Petr V. Nazarov, Tony Kaoma, Maryna Chepeleva", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installing and loading the package", "Example dataset", "Consensus independent component analysis", "Enrichment analysis", "Survival analysis", "Automatic report generation", "Session info", "References" ], "created": "2022-04-01 00:18:59", "modified": "2023-09-18 08:22:33", "commits": 10 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "consica", "_universes": [ "bioc", "biomod-lih" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.11.0", "date": "2026-07-04T04:00:43.000Z", "distro": "resolute", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/4c77285583b68e390d6d1e555c65668692ba91e801b541ec353bd7845aa91b44", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.6.1", "os": "linux", "version": "2.11.0", "date": "2026-07-04T04:00:24.000Z", "distro": "resolute", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/b233aa81170f82c5135ac8e3e805abcf8b6ac805021d740baa60f1a1d47a5949", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.5.3", "os": "mac", "version": "2.11.0", "date": "2026-07-04T03:58:28.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/23f40df509a96d28676b2200308eb54badc748f515be3972afb03089796446fb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.6.1", "os": "mac", "version": "2.11.0", "date": "2026-07-04T03:58:50.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/38a7ba7aad734138c0ba9b6f93e3375f02e3da8ecc402754144efb3da81d24a4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.6.0", "os": "wasm", "version": "2.11.0", "date": "2026-07-04T04:00:52.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/47131103a463f9c6f0777ab846ab2b70d81434e353b0fb596094bb5e7faa69e4", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.7.0", "os": "win", "version": "2.11.0", "date": "2026-07-04T03:58:57.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/0b4b1caa31d10010b36eb37d811b0a09b006ad9a774ac233b02d820b583e8632", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.5.3", "os": "win", "version": "2.11.0", "date": "2026-07-04T03:59:31.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/7fe89897f124e6d28e018a70f2d796564decf2e3586bdd2ed7d93ca144c858e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" }, { "r": "4.6.1", "os": "win", "version": "2.11.0", "date": "2026-07-04T03:59:02.000Z", "commit": "6e95b58cc99f6963ccccb601d6db6254502cb5b4", "fileid": "https://r2.ropensci.org/7f7ad823e5c453f3ceb05e365756d0f8ccb69ee4ff742cd79232b263f595dd22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694043452" } ] }