{ "_id": "6a494e6af6c47c441949a192", "Package": "omicade4", "Type": "Package", "Title": "Multiple co-inertia analysis of omics datasets", "Version": "1.53.0", "Date": "2020-10-26", "Author": "Chen Meng, Aedin Culhane, Amin M. Gholami.", "Maintainer": "Chen Meng ", "Description": "This package performes multiple co-inertia analysis of\nomics datasets.", "Reference": "Meng C, Kuster B, Culhane AC and Gholami AM. A multivariate\napproach to the integration of multi-omics datasets. BMC\nBioinformatics (2014) (Manuscript accepted) Culhane AC,\nThioulouse J, Perriere G, Higgins DG. (2005) MADE4: an R\npackage for multivariate analysis of gene expression\ndata.Bioinformatics. 21(11):2789-90. S. Dray and A.B. Dufour.\n(2007) The ade4 package: implementing the duality diagram for\necologists. Journal of Statistical Software 22(4):1-20.", "License": "GPL-2", "LazyLoad": "yes", "Packaged": { "Date": "2026-07-03 23:25:32 UTC", "User": "root" }, "biocViews": "Software, Clustering, Classification, MultipleComparison", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:11 UTC", "RemoteUrl": "https://github.com/bioc/omicade4", "RemoteRef": "HEAD", "RemoteSha": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "omicade4_1.53.0.tar.gz", "_fileid": "https://r2.ropensci.org/d8ebf470467330312901ddc09c425ac9dd952f57963370da702a496ba18e4361", "_filesize": 684764, "_sha256": "d8ebf470467330312901ddc09c425ac9dd952f57963370da702a496ba18e4361", "_expires": "2026-10-12T18:18:17.000Z", "_created": "2026-07-03T23:25:32.000Z", "_published": "2026-07-04T18:18:18.750Z", "_bioccheck": { "error": 1, "warning": 2, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862", "_status": "success", "_upstream": "https://github.com/bioc/omicade4", "_commit": { "id": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379891 }, "_maintainer": { "name": "Chen Meng", "email": "mengchen18@gmail.com", "login": "mengchen18", "description": "", "uuid": 4140432 }, "_distro": "resolute", "_jobs": [ { "job": 85155619839, "time": 173, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8076128488" }, { "job": 85155619731, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8076142979" }, { "job": 85155619865, "time": 249, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8076139031" }, { "job": 85155619828, "time": 118, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8076120195" }, { "job": 85155619797, "time": 135, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8076122752" }, { "job": 85155619531, "time": 234, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8076102672" }, { "job": 85155619679, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8076123374" }, { "job": 85155619826, "time": 179, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8076129342" }, { "job": 85155619804, "time": 167, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8076127425" }, { "job": 85155619750, "time": 178, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8076128934" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "ade4", "role": "Depends" }, { "package": "made4", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.53.0", "bioc": "3.24" }, { "branch": "release", "version": "1.52.0", "bioc": "3.23" } ], "_topics": [ "software", "clustering", "classification", "multiplecomparison" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 12, "_searchresults": 61, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/omicade4.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "mcia", "plot.mcia", "plotVar", "selectVar", "topVar" ], "_datasets": [ { "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": "omicade4-package", "title": "multiple co-inertia analysis of omics datasets", "topics": [ "omicade4-package", "omicade4" ] }, { "page": "mcia", "title": "multiple co-inertia analysis", "topics": [ "mcia", "plot.mcia" ] }, { "page": "NCI60_4arrays", "title": "Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms", "topics": [ "NCI60_4arrays" ] }, { "page": "plotVar", "title": "Plot variable (gene) spaces of result from MCIA or CIA", "topics": [ "plotVar" ] }, { "page": "plotVar.cia", "title": "Plot variable space of result from 'cia'", "topics": [ "plotVar.cia" ] }, { "page": "plotVar.mcia", "title": "Plot variable space of result from 'mcia'", "topics": [ "plotVar.mcia" ] }, { "page": "selectVar", "title": "Selecting variables (genes) from result of MCIA or CIA according to co-ordinates", "topics": [ "selectVar" ] }, { "page": "selectVar.cia", "title": "Selecting variables from result of CIA", "topics": [ "selectVar.cia" ] }, { "page": "selectVar.mcia", "title": "Selecting variables from result of MCIA", "topics": [ "selectVar.mcia" ] }, { "page": "topVar", "title": "Selecting top weighted variables (genes) from result of MCIA or CIA", "topics": [ "topVar" ] }, { "page": "topVar.cia", "title": "Selecting top weighted variables (genes) from result of CIA", "topics": [ "topVar.cia" ] }, { "page": "topVar.mcia", "title": "Selecting top weighted variables (genes) from result of MCIA", "topics": [ "topVar.mcia" ] } ], "_rundeps": [ "abind", "ade4", "Biobase", "BiocGenerics", "bitops", "caTools", "DelayedArray", "generics", "GenomicRanges", "gplots", "gtools", "IRanges", "KernSmooth", "lattice", "made4", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "pixmap", "RColorBrewer", "Rcpp", "RcppArmadillo", "S4Arrays", "S4Vectors", "scatterplot3d", "Seqinfo", "sp", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "omicade4.Rnw", "filename": "omicade4.pdf", "title": "Using omicade4", "engine": "utils::Sweave", "headings": [ "1 Introduction", "2 Quick Start" ], "created": "2013-10-23 21:39:47", "modified": "2013-11-27 18:43:59", "commits": 3 } ], "_score": 5.563481085394411, "_indexed": true, "_nocasepkg": "omicade4", "_universes": [ "bioc", "mengchen18" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.53.0", "date": "2026-07-03T23:28:48.000Z", "distro": "resolute", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/bd4ed77a862f4220a0ba46181fc530259cb7ea3d94dd9c89a8a79afcf492c7f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.6.1", "os": "linux", "version": "1.53.0", "date": "2026-07-03T23:28:24.000Z", "distro": "resolute", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/23d2c3d457ede980009d8900794687ee6a2f66315f5af94fb3e5ab6952b778d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.5.3", "os": "mac", "version": "1.53.0", "date": "2026-07-03T23:27:06.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/f3224a2ba60e706d4893532ea0f6a858f5e76b74abd0188961f2156d152e4c77", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.6.1", "os": "mac", "version": "1.53.0", "date": "2026-07-03T23:27:17.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/1197676cf2bcccdf8164d18de118329baffb64d0d87593ae91f6e9f43abf8095", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.6.0", "os": "wasm", "version": "1.53.0", "date": "2026-07-03T23:28:24.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/a1fe1a1feb7a4b8afdcb3d2423b5bcbb104c6b9c310d2d8b1392ce3050352cbf", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.7.0", "os": "win", "version": "1.53.0", "date": "2026-07-03T23:27:11.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/926e4bac5400e01ed118f5b213ca6d688d8fecdd388764dbe8ce1ac6b4493a25", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.5.3", "os": "win", "version": "1.53.0", "date": "2026-07-03T23:26:55.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/cc700f4e2b7c0a148812d76e698d9865bb5931ed8c8d96a74d11381ecdce6e7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" }, { "r": "4.6.1", "os": "win", "version": "1.53.0", "date": "2026-07-03T23:27:09.000Z", "commit": "ac65c4e81017b0f97141405bb95eb3b3180191bf", "fileid": "https://r2.ropensci.org/b8c0e0437d67a692477af277dba9508a09caf76d9fa28f440a869fd0ec355b3f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28687577862" } ] }