{ "_id": "6a4a658a1e9cffeb4b83392d", "Package": "RUVSeq", "Version": "1.47.0", "Title": "Remove Unwanted Variation from RNA-Seq Data", "Description": "This package implements the remove unwanted variation\n(RUV) methods of Risso et al. (2014) for the normalization of\nRNA-Seq read counts between samples.", "Authors@R": "c(person(\"Davide\", \"Risso\", email = \"risso.davide@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\")),\nperson(\"Sandrine\", \"Dudoit\", role = \"aut\"),\nperson(\"Lorena\", \"Pantano\", role = \"ctb\"),\nperson(\"Kamil\", \"Slowikowski\", role = \"ctb\"))", "Author": "Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena\nPantano [ctb], Kamil Slowikowski [ctb]", "Maintainer": "Davide Risso ", "Date": "04-15-2014", "VignetteBuilder": "knitr", "License": "Artistic-2.0", "LazyLoad": "yes", "biocViews": "ImmunoOncology, DifferentialExpression, Preprocessing,\nRNASeq, Software", "URL": "https://github.com/drisso/RUVSeq", "BugReports": "https://github.com/drisso/RUVSeq/issues", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "make libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:14 UTC", "RemoteUrl": "https://github.com/bioc/RUVSeq", "RemoteRef": "HEAD", "RemoteSha": "32653544258f866b815916e9dbaddf8a6a8bcc27", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-05 13:59:54 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "RUVSeq_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/2e7df94d82d50f4284920f263b865845fa9b9e58e383f01dd55d6142529a4fe0", "_filesize": 429989, "_sha256": "2e7df94d82d50f4284920f263b865845fa9b9e58e383f01dd55d6142529a4fe0", "_expires": "2026-10-13T14:09:12.000Z", "_created": "2026-07-05T13:59:54.000Z", "_published": "2026-07-05T14:09:14.213Z", "_bioccheck": { "error": 1, "warning": 2, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978", "_status": "success", "_upstream": "https://github.com/bioc/RUVSeq", "_commit": { "id": "32653544258f866b815916e9dbaddf8a6a8bcc27", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379954 }, "_maintainer": { "name": "Davide Risso", "email": "risso.davide@gmail.com", "login": "drisso", "description": "", "uuid": 8451432 }, "_distro": "resolute", "_jobs": [ { "job": 85229666832, "time": 217, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8092512088" }, { "job": 85229666865, "time": 409, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8092535728" }, { "job": 85229666856, "time": 485, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8092545302" }, { "job": 85229666862, "time": 226, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8092520135" }, { "job": 85229666846, "time": 227, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8092519988" }, { "job": 85229270087, "time": 329, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8092483049" }, { "job": 85229666849, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8092509431" }, { "job": 85229666840, "time": 388, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8092533046" }, { "job": 85229666844, "time": 313, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8092524133" }, { "job": 85229666845, "time": 369, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8092531020" } ], "_registered": true, "_dependencies": [ { "package": "Biobase", "role": "Depends" }, { "package": "EDASeq", "version": ">= 1.99.1", "role": "Depends" }, { "package": "edgeR", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "zebrafishRNASeq", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 5, "_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": [ "immunooncology", "differentialexpression", "preprocessing", "rnaseq", "software" ], "_stars": 15, "_contributors": [ { "user": "drisso", "count": 26, "uuid": 8451432 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "dtenenba", "count": 10, "uuid": 2286826 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 91, "_devurl": "https://github.com/drisso/ruvseq", "_searchresults": 800, "_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/readme.html", "extra/readme.md", "extra/RUVSeq.html", "manual.pdf" ], "_homeurl": "https://github.com/drisso/ruvseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "makeGroups", "RUVg", "RUVr", "RUVs" ], "_help": [ { "page": "RUVSeq-package", "title": "Remove Unwanted Variation from RNA-Seq Data", "topics": [ "RUVSeq-package", "RUVSeq" ] }, { "page": "makeGroups", "title": "Make a matrix suitable for use with RUVSeq methods such as 'RUVs'.", "topics": [ "makeGroups" ] }, { "page": "residuals.DGEGLM", "title": "Deviance and Pearson Residuals for the Negative Binomial Model of 'edgeR'", "topics": [ "residuals.DGEGLM" ] }, { "page": "RUVg", "title": "Remove Unwanted Variation Using Control Genes", "topics": [ "RUVg", "RUVg,matrix,ANY,numeric-method", "RUVg,SeqExpressionSet,character,numeric-method", "RUVg-methods" ] }, { "page": "RUVr", "title": "Remove Unwanted Variation Using Residuals", "topics": [ "RUVr", "RUVr,matrix,ANY,numeric,matrix-method", "RUVr,SeqExpressionSet,character,numeric,matrix-method", "RUVr-methods" ] }, { "page": "RUVs", "title": "Remove Unwanted Variation Using Replicate/Negative Control Samples", "topics": [ "RUVs", "RUVs,matrix,ANY,numeric,matrix-method", "RUVs,SeqExpressionSet,character,numeric,matrix-method", "RUVs-methods" ] } ], "_readme": "https://github.com/bioc/RUVSeq/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "aroma.light", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "deldir", "dplyr", "EDASeq", "edgeR", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "hwriter", "interp", "IRanges", "jpeg", "jsonlite", "KEGGREST", "lambda.r", "lattice", "latticeExtra", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "pwalign", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "ShortRead", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "RUVSeq.Rmd", "filename": "RUVSeq.html", "title": "RUVSeq: Remove Unwanted Variation from RNA-Seq Data", "author": "Davide Risso", "engine": "knitr::rmarkdown", "headings": [ "Overview", "A typical differential expression analysis workflow", "Filtering and exploratory data analysis", "RUVg: Estimating the factors of unwanted variation using control genes", "Differential expression analysis", "Empirical control genes", "Differential expression analysis with DESeq2", "RUVs: Estimating the factors of unwanted variation using replicate samples}", "RUVr: Estimating the factors of unwanted variation using residuals", "Session info", "References" ], "created": "2022-11-22 10:09:10", "modified": "2022-11-22 10:09:10", "commits": 1 } ], "_score": 10.03342375548695, "_indexed": true, "_nocasepkg": "ruvseq", "_universes": [ "bioc", "drisso" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-07-05T14:04:01.000Z", "distro": "resolute", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/f2e812a7d0b371e8524ac5f06fb4633723892faf509289a67487848f70c706f4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-07-05T14:04:52.000Z", "distro": "resolute", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/fe1fc0c787fc2c3c72791ffd93f20949d84b55c70aecbd320832e35fff5faa7b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-07-05T14:03:06.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/efc6c38e10423aa0081c9e10eb2b8515e9dbeeb6ae842d25cf64fc6411554eb9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-07-05T14:03:05.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/60b2903c6184094ec3ff8ab3f1f0ca9da147736c34bc0182e9b0510d5b3208b8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-07-05T14:03:56.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/f878b51c7c7d4f6ab888ed1190f807634344748452ebf80315ef7f29a04c9c03", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-07-05T14:02:14.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/df360fe7ce3708b05c95be1a5c52c06793273d8eb069bd45532b44788617e1d3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-07-05T14:02:01.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/8cacf9dcfac47d806680ca96813520211bf471a7921f75c62f343bbe0f37b523", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-07-05T14:02:19.000Z", "commit": "32653544258f866b815916e9dbaddf8a6a8bcc27", "fileid": "https://r2.ropensci.org/a74625d7f678f97fca5ba1b9c103802176fd5ec2cc69fcc1d7955815d45184e2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28743096978" } ] }