{ "_id": "6a1ac1da1d7bb097a09d8ead", "Package": "mogsa", "Type": "Package", "Title": "Multiple omics data integrative clustering and gene set analysis", "Version": "1.47.0", "Date": "2020-06-04", "Author": "Chen Meng", "Maintainer": "Chen Meng ", "Description": "This package provide a method for doing gene set analysis\nbased on multiple omics data.", "License": "GPL-2", "VignetteBuilder": "knitr", "biocViews": "GeneExpression, PrincipalComponent, StatisticalMethod,\nClustering, Software", "NeedsCompilation": "no", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:03 UTC", "RemoteUrl": "https://github.com/bioc/mogsa", "RemoteRef": "HEAD", "RemoteSha": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "Packaged": { "Date": "2026-05-30 07:31:36 UTC", "User": "root" }, "MD5sum": "b58f46bfdb6e73905ed64ccec19865ee", "_user": "bioc", "_type": "src", "_file": "mogsa_1.47.0.tar.gz", "_fileid": "8ef6139c2cb19774f01bcbcf025f8dd603da55666f9c6609bf585fa3f5491ac7", "_filesize": 1009106, "_sha256": "8ef6139c2cb19774f01bcbcf025f8dd603da55666f9c6609bf585fa3f5491ac7", "_created": "2026-05-30T07:31:36.000Z", "_published": "2026-05-30T10:54:18.845Z", "_jobs": [ { "job": 78633734081, "time": 164, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306510951" }, { "job": 78633734078, "time": 269, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306522652" }, { "job": 78633734088, "time": 294, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306525247" }, { "job": 78633734105, "time": 194, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307627329" }, { "job": 78633734092, "time": 191, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307627056" }, { "job": 78633456825, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306492738" }, { "job": 78633734121, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306508062" }, { "job": 78633734085, "time": 212, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306516423" }, { "job": 78633734083, "time": 197, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306514880" }, { "job": 78633734080, "time": 215, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306516676" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/mogsa", "_commit": { "id": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380063 }, "_maintainer": { "name": "Chen Meng", "email": "mengchen18@gmail.com", "login": "mengchen18", "description": "", "uuid": 4140432 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "graphite", "role": "Imports" }, { "package": "genefilter", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "GSEABase", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "svd", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "principalcomponent", "statisticalmethod", "clustering", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 591, "source": "https://www.bioconductor.org/packages/stats/bioc/mogsa" }, "_mentions": 1, "_searchresults": 58, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mogsa.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotate.gs", "bootMbpca", "bootMoa", "box.gs.feature", "combine", "decompose.gs.group", "decompose.gs.ind", "distMoa", "getmgsa", "GIS", "matpower", "mbpca", "moa", "moaCoef", "moaScore", "moGap", "mogsa", "pairwise.rv", "plot", "plotGS", "prepGraphite", "prepMsigDB", "prepSupMoa", "print", "show", "softK", "summary", "sup.moa", "wsvd" ], "_datasets": [ { "name": "NCI60_4array_supdata", "title": "supp data for Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms", "object": "NCI60_4array_supdata", "file": "NCI60_4array_supdata.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "NCI60_4arrays", "title": "Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms", "object": "NCI60_4arrays", "file": "NCI60_4arrays.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "mogsa-package", "title": "Multiple omics clustering and gene set analysis", "topics": [ "mogsa-package" ] }, { "page": "annotate.gs", "title": "Summary annotation information of a gene set", "topics": [ "annotate.gs" ] }, { "page": "biSoftK", "title": "NIPALS algorithm with soft thresholding operator on rows and columns", "topics": [ "biSoftK" ] }, { "page": "bootMbpca", "title": "Bootstrap mbpca to estimate the coherence of different data sets", "topics": [ "bootMbpca" ] }, { "page": "bootMbpcaK", "title": "An internal function called by 'bootMbpca'.", "topics": [ "bootMbpcaK" ] }, { "page": "bootMoa", "title": "Significant components in \"moa\" returned by function \"moa\".", "topics": [ "bootMoa" ] }, { "page": "box.gs.feature", "title": "boxplot of gene set variables across all samples.", "topics": [ "box.gs.feature" ] }, { "page": "combine-methods", "title": "Combine two objects of class 'mgsa' into one.", "topics": [ "combine", "combine,mgsa,mgsa-method", "combine-methods" ] }, { "page": "decompose.gs.group", "title": "Data-wise or PC-wise decomposition of gene set scores for all observations.", "topics": [ "decompose.gs.group" ] }, { "page": "decompose.gs.ind", "title": "Data-wise or PC-wise decomposition of gene set scores for a single observation.", "topics": [ "decompose.gs.ind" ] }, { "page": "deflat", "title": "deflat function used by 'mbpca'", "topics": [ "deflat" ] }, { "page": "distMoa", "title": "Calculate the distance matrix from an object of class 'moa-class'.", "topics": [ "distMoa" ] }, { "page": "getmgsa", "title": "get values in an object of class \"mgsa\".", "topics": [ "getmgsa" ] }, { "page": "GIS", "title": "calculate gene influential scores of genes in a gene set.", "topics": [ "GIS" ] }, { "page": "matpower", "title": "compute the power of a matrix", "topics": [ "matpower" ] }, { "page": "mbpca", "title": "Extension of PCA to analyze multiple data sets", "topics": [ "mbpca" ] }, { "page": "mgsa-class", "title": "Class '\"mgsa\"'", "topics": [ "mgsa-class" ] }, { "page": "moa", "title": "Multiple omics data analysis using MFA or STATIS", "topics": [ "moa" ] }, { "page": "moa-class", "title": "Class '\"moa\"'", "topics": [ "moa-class", "plot,moa,missing-method" ] }, { "page": "moa.sup-class", "title": "Class '\"moa.sup\"'", "topics": [ "moa.sup-class" ] }, { "page": "moaCoef", "title": "Extract the loadings/coefficients from an object of class 'moa-class'.", "topics": [ "moaCoef" ] }, { "page": "moaScore", "title": "Extract global scores from an object of class 'moa-class'.", "topics": [ "moaScore" ] }, { "page": "moGap", "title": "Gap statistic for clustering latent variables in 'moa-class'.", "topics": [ "moGap" ] }, { "page": "mogsa", "title": "multiple omics data integration and gene set analysis", "topics": [ "mogsa" ] }, { "page": "msvd", "title": "SVD based algorithm to calculate block Score and global scores for 'mbpca'.", "topics": [ "msvd" ] }, { "page": "NCI60_4array_supdata", "title": "supp data for Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms", "topics": [ "NCI60_4array_supdata" ] }, { "page": "NCI60_4arrays", "title": "Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms", "topics": [ "NCI60_4arrays" ] }, { "page": "nipalsSoftK", "title": "NIPALS algorithm with soft thresholding operator", "topics": [ "nipalsSoftK" ] }, { "page": "pairwise.rv", "title": "pairwise RV coefficients.", "topics": [ "pairwise.rv" ] }, { "page": "plot-methods", "title": "Methods for function 'plot'", "topics": [ "plot-methods" ] }, { "page": "plotGS", "title": "Plot the gene set space", "topics": [ "plotGS" ] }, { "page": "prepGraphite", "title": "Prepare pathway gene sets from graphite package", "topics": [ "prepGraphite" ] }, { "page": "prepMsigDB", "title": "Conver gmt format file to a list", "topics": [ "prepMsigDB" ] }, { "page": "prepSupMoa", "title": "Prepare sumpplementary tables for projection by sup.moa or mogsa.", "topics": [ "prepSupMoa" ] }, { "page": "print-methods", "title": "Methods for function 'print'", "topics": [ "print", "print,mgsa-method", "print,moa-method", "print,moa.sup-method", "print-methods" ] }, { "page": "processOpt", "title": "preprocessing of input data in 'mbpca'.", "topics": [ "processOpt" ] }, { "page": "show-methods", "title": "Methods for function 'show'", "topics": [ "show", "show,mgsa-method", "show,moa-method", "show,moa.sup-method", "show-methods" ] }, { "page": "softK", "title": "Soft-thresholding operator", "topics": [ "softK" ] }, { "page": "summary-methods", "title": "Methods for function 'summary'", "topics": [ "summary", "summary,mgsa-method", "summary,moa-method", "summary,moa.sup-method", "summary-methods" ] }, { "page": "sup.moa", "title": "Projecting supplementary tables on object of class 'moa-class'.", "topics": [ "sup.moa" ] }, { "page": "toMoa", "title": "convert 'mbpca' result to 'moa-class'", "topics": [ "toMoa" ] }, { "page": "wsvd", "title": "Weighted singular value decomposition (SVD)", "topics": [ "wsvd" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "caTools", "cli", "cluster", "corpcor", "cpp11", "crayon", "curl", "DBI", "dir.expiry", "fastmap", "filelock", "genefilter", "generics", "glue", "gplots", "graph", "graphite", "GSEABase", "gtools", "httr", "IRanges", "jsonlite", "KEGGREST", "KernSmooth", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "purrr", "R6", "rappdirs", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "survival", "svd", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "moCluster-knitr.Rnw", "filename": "moCluster-knitr.pdf", "title": "moCluster: Integrative clustering using multiple omics data", "engine": "knitr::knitr", "headings": [], "created": "2019-05-07 11:32:37", "modified": "2019-05-07 11:32:37", "commits": 1 }, { "source": "mogsa-knitr.Rnw", "filename": "mogsa-knitr.pdf", "title": "mogsa: gene set analysis on multiple omics data", "engine": "knitr::knitr", "headings": [], "created": "2019-05-07 11:32:37", "modified": "2019-05-07 11:32:37", "commits": 1 } ], "_score": 4.365487984890899, "_indexed": true, "_nocasepkg": "mogsa", "_universes": [ "bioc", "mengchen18" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-30T07:35:02.000Z", "distro": "noble", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "a26b623fc41d28e7718d074170950263365d8d844541ca5702d03cdc0625ea74", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-30T07:35:12.000Z", "distro": "noble", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "764be8da3e852deaa4eebe4ee88c17a1a547ff9dfefc983c81ba41e441cec284", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-30T10:46:44.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "9543180c6b870eaf4d1dba1013bd64b0a563bfb3bc9d42244fa7f55b83a6c1d4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-30T10:46:35.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "e4106c2e5e6c73c79c818e08429463d42b165c36bb8ed17e8e999aac9be1790b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-05-30T07:34:24.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "74ed0b568c42bb04c93551b7a9c0773b28d6fa1706b53ff483e47c616d0070f5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-05-30T07:33:34.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "3d2e7b3a5de74245d2e5120c6f36db5263f6b3ed18faf28d6f77f197cee4a17f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-05-30T07:33:29.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "9bcb7023ae89af48ad6d71f310617d74fd88811d6a8661042ab356f678bda52b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-05-30T07:33:48.000Z", "commit": "2a0cde2c29246ce82ddf3045687888f9fcd01df3", "fileid": "d1a592b888dc4cef4436177540f6b81658fa317178b1e2a8631372141b87e167", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678052238" } ] }