{ "_id": "6a493e57a19c9318096e7ade", "Package": "consensus", "Title": "Cross-platform consensus analysis of genomic measurements via\ninterlaboratory testing method", "Version": "1.31.0", "Date": "2020-05-22", "Author": "Tim Peters", "Maintainer": "Tim Peters ", "Authors@R": "c(person(\"Tim\", \"Peters\", role = c(\"cre\", \"aut\"),\nemail = \"t.peters@garvan.org.au\"),\nperson(\"Benedetta Frida\", \"Baldi\", role = \"art\",\nemail = \"b.baldi@garvan.org.au\"))", "Description": "An implementation of the American Society for Testing and\nMaterials (ASTM) Standard E691 for interlaboratory testing\nprocedures, designed for cross-platform genomic measurements.\nGiven three (3) or more genomic platforms or laboratory\nprotocols, this package provides interlaboratory testing\nprocedures giving per-locus comparisons for sensitivity and\nprecision between platforms.", "biocViews": "QualityControl, Regression, DataRepresentation,\nGeneExpression, Microarray, RNASeq", "License": "BSD_3_clause + file LICENSE", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:48:24 UTC", "RemoteUrl": "https://github.com/bioc/consensus", "RemoteRef": "HEAD", "RemoteSha": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 03:24:57 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "consensus_1.31.0.tar.gz", "_fileid": "https://r2.ropensci.org/13d665e0ce11fc996d15b70c2fe8e9943de950af9a15c8c0a9861c50d2c40f95", "_filesize": 1169797, "_sha256": "13d665e0ce11fc996d15b70c2fe8e9943de950af9a15c8c0a9861c50d2c40f95", "_expires": "2026-10-12T17:09:42.000Z", "_created": "2026-07-04T03:24:57.000Z", "_published": "2026-07-04T17:09:43.962Z", "_bioccheck": { "error": 0, "warning": 2, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918", "_status": "success", "_upstream": "https://github.com/bioc/consensus", "_commit": { "id": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380504 }, "_maintainer": { "name": "Tim Peters", "email": "t.peters@garvan.org.au", "login": "timpeters82", "description": "", "uuid": 5061381 }, "_distro": "resolute", "_jobs": [ { "job": 85150946355, "time": 173, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8077885629" }, { "job": 85150946488, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8077889252" }, { "job": 85150946369, "time": 211, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8077890096" }, { "job": 85150946411, "time": 87, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8077875973" }, { "job": 85150946398, "time": 84, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8077875496" }, { "job": 85150946114, "time": 157, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8077865451" }, { "job": 85150946432, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8077878281" }, { "job": 85150946484, "time": 70, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8077874185" }, { "job": 85150946347, "time": 102, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8077878235" }, { "job": 85150946494, "time": 75, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8077874767" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "RColorBrewer", "role": "Depends" }, { "package": "matrixStats", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23" } ], "_topics": [ "qualitycontrol", "regression", "datarepresentation", "geneexpression", "microarray", "rnaseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 5, "_searchresults": 8, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/consensus.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "fitConsensus", "MultiMeasure", "plotMarginals", "plotMostDiscordant", "plotOneFit" ], "_datasets": [ { "name": "Agilent", "title": "Agilent microarray gene expression data", "object": "TCGA", "file": "TCGA.RData", "class": [ "matrix", "array" ], "fields": [ "TCGA.06.0211.01B.01", "TCGA.06.0190.01A.01", "TCGA.06.0238.01A.02", "TCGA.06.0645.01A.01", "TCGA.06.0132.01A.02", "TCGA.12.0618.01A.01", "TCGA.06.0178.01A.01", "TCGA.02.0047.01A.01", "TCGA.06.0174.01A.01", "TCGA.12.0616.01A.01", "TCGA.06.0184.01A.01", "TCGA.06.0168.01A.01", "TCGA.06.0644.01A.02", "TCGA.06.0157.01A.01", "TCGA.06.0130.01A.01", "TCGA.06.0158.01A.01", "TCGA.06.0646.01A.01", "TCGA.08.0386.01A.01", "TCGA.06.0129.01A.01", "TCGA.06.0138.01A.02", "TCGA.06.0125.01A.01", "TCGA.06.0219.01A.01", "TCGA.06.0139.01A.01", "TCGA.12.0619.01A.01", "TCGA.02.0055.01A.01", "TCGA.06.0210.01A.01", "TCGA.06.0187.01A.01" ], "rows": 1000, "table": true, "tojson": true }, { "name": "Huex", "title": "Affymetrix Huex gene expression data", "object": "TCGA", "file": "TCGA.RData", "class": [ "matrix", "array" ], "fields": [ "TCGA.06.0211.01B.01", "TCGA.06.0190.01A.01", "TCGA.06.0238.01A.02", "TCGA.06.0645.01A.01", "TCGA.06.0132.01A.02", "TCGA.12.0618.01A.01", "TCGA.06.0178.01A.01", "TCGA.02.0047.01A.01", "TCGA.06.0174.01A.01", "TCGA.12.0616.01A.01", "TCGA.06.0184.01A.01", "TCGA.06.0168.01A.01", "TCGA.06.0644.01A.02", "TCGA.06.0157.01A.01", "TCGA.06.0130.01A.01", "TCGA.06.0158.01A.01", "TCGA.06.0646.01A.01", "TCGA.08.0386.01A.01", "TCGA.06.0129.01A.01", "TCGA.06.0138.01A.02", "TCGA.06.0125.01A.01", "TCGA.06.0219.01A.01", "TCGA.06.0139.01A.01", "TCGA.12.0619.01A.01", "TCGA.02.0055.01A.01", "TCGA.06.0210.01A.01", "TCGA.06.0187.01A.01" ], "rows": 1000, "table": true, "tojson": true }, { "name": "RNASeq", "title": "RNA-Seq gene expression data", "object": "TCGA", "file": "TCGA.RData", "class": [ "matrix", "array" ], "fields": [ "TCGA.06.0211.01B.01", "TCGA.06.0190.01A.01", "TCGA.06.0238.01A.02", "TCGA.06.0645.01A.01", "TCGA.06.0132.01A.02", "TCGA.12.0618.01A.01", "TCGA.06.0178.01A.01", "TCGA.02.0047.01A.01", "TCGA.06.0174.01A.01", "TCGA.12.0616.01A.01", "TCGA.06.0184.01A.01", "TCGA.06.0168.01A.01", "TCGA.06.0644.01A.02", "TCGA.06.0157.01A.01", "TCGA.06.0130.01A.01", "TCGA.06.0158.01A.01", "TCGA.06.0646.01A.01", "TCGA.08.0386.01A.01", "TCGA.06.0129.01A.01", "TCGA.06.0138.01A.02", "TCGA.06.0125.01A.01", "TCGA.06.0219.01A.01", "TCGA.06.0139.01A.01", "TCGA.12.0619.01A.01", "TCGA.02.0055.01A.01", "TCGA.06.0210.01A.01", "TCGA.06.0187.01A.01" ], "rows": 1000, "table": true, "tojson": true }, { "name": "U133A", "title": "Affymetrix U133A gene expression data", "object": "TCGA", "file": "TCGA.RData", "class": [ "matrix", "array" ], "fields": [ "TCGA.06.0211.01B.01", "TCGA.06.0190.01A.01", "TCGA.06.0238.01A.02", "TCGA.06.0645.01A.01", "TCGA.06.0132.01A.02", "TCGA.12.0618.01A.01", "TCGA.06.0178.01A.01", "TCGA.02.0047.01A.01", "TCGA.06.0174.01A.01", "TCGA.12.0616.01A.01", "TCGA.06.0184.01A.01", "TCGA.06.0168.01A.01", "TCGA.06.0644.01A.02", "TCGA.06.0157.01A.01", "TCGA.06.0130.01A.01", "TCGA.06.0158.01A.01", "TCGA.06.0646.01A.01", "TCGA.08.0386.01A.01", "TCGA.06.0129.01A.01", "TCGA.06.0138.01A.02", "TCGA.06.0125.01A.01", "TCGA.06.0219.01A.01", "TCGA.06.0139.01A.01", "TCGA.12.0619.01A.01", "TCGA.02.0055.01A.01", "TCGA.06.0210.01A.01", "TCGA.06.0187.01A.01" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "consensus-package", "title": "Cross-platform consensus analysis of genomic measurements via interlaboratory testing method", "topics": [ "consensus-package", "consensus" ] }, { "page": "Agilent", "title": "Agilent microarray gene expression data", "topics": [ "Agilent" ] }, { "page": "ConsensusFit-class", "title": "Row-linear fit from multiple platforms/conditions - class", "topics": [ "ConsensusFit-class" ] }, { "page": "fitConsensus", "title": "Fit row-linear models to all loci", "topics": [ "fitConsensus" ] }, { "page": "Huex", "title": "Affymetrix Huex gene expression data", "topics": [ "Huex" ] }, { "page": "MultiMeasure", "title": "MultiMeasure Constructor", "topics": [ "MultiMeasure" ] }, { "page": "MultiMeasure-class", "title": "Multi-platform genomic measurements across the same samples - class", "topics": [ "MultiMeasure-class" ] }, { "page": "plotMarginals", "title": "Density plots of per-platform marginal distributions", "topics": [ "plotMarginals" ] }, { "page": "plotMostDiscordant", "title": "Plot a heatmap showing a selection of loci", "topics": [ "plotMostDiscordant" ] }, { "page": "plotOneFit", "title": "Plot a single row-linear fit from a genomic locus", "topics": [ "plotOneFit" ] }, { "page": "RNASeq", "title": "RNA-Seq gene expression data", "topics": [ "RNASeq" ] }, { "page": "U133A", "title": "Affymetrix U133A gene expression data", "topics": [ "U133A" ] } ], "_readme": "https://github.com/bioc/consensus/raw/HEAD/README.md", "_rundeps": [ "bitops", "caTools", "gplots", "gtools", "KernSmooth", "matrixStats", "RColorBrewer" ], "_vignettes": [ { "source": "consensus.Rnw", "filename": "consensus.pdf", "title": "Fitting and visualising row-linear models with \\texttt{consensus}", "engine": "knitr::knitr", "headings": [], "created": "2018-05-16 06:42:00", "modified": "2018-07-23 06:01:56", "commits": 3 } ], "_score": 4.698970004336019, "_indexed": true, "_nocasepkg": "consensus", "_universes": [ "bioc", "timpeters82" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-07-04T03:28:19.000Z", "distro": "resolute", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/31829e042454a4d5ea7a1ff97cf1bd63d4db8fc3026d4d57c4e1331c2f5f0061", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.6.1", "os": "linux", "version": "1.31.0", "date": "2026-07-04T03:28:26.000Z", "distro": "resolute", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/10de966c05eb4f9171dcbfc0abbf7b5617a5a5605247ad7993cf361e868da6c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", "date": "2026-07-04T03:26:28.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/91b259c51391e23802eacf91b5becd1c2a26a78e579285b1ae8c46cd1a9ff4c8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.6.1", "os": "mac", "version": "1.31.0", "date": "2026-07-04T03:26:21.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/3a3d56d584ca532df8099f8ec2dfc655cf5ff519ee08faca4f57555a4cab7d87", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.6.0", "os": "wasm", "version": "1.31.0", "date": "2026-07-04T03:26:56.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/12299142d17a1e9b1171a30e4dab255ce24b038249d9b224dda6ef920c9fc2f1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.7.0", "os": "win", "version": "1.31.0", "date": "2026-07-04T03:26:01.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/5445a4d01ad4645d4f80dc12aa55166f6bb7192a714c6eb7f0f6b5a50e4b4fd1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.5.3", "os": "win", "version": "1.31.0", "date": "2026-07-04T03:26:36.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/9a19afd5d197710d053cfed9c4213275deea03c7a457a2503a36550e919d03d2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" }, { "r": "4.6.1", "os": "win", "version": "1.31.0", "date": "2026-07-04T03:26:07.000Z", "commit": "98fe0b03397b6431e589250c0bfe25a5188f54b2", "fileid": "https://r2.ropensci.org/c5b07b415594b2e0e12cdb9db86975aa01e087304f2f7123301b84e3b2ef2d8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28693393918" } ] }