{ "_id": "6a1b04541d7bb097a0a0255b", "Package": "yarn", "Title": "YARN: Robust Multi-Condition RNA-Seq Preprocessing and\nNormalization", "Version": "1.38.0", "Authors@R": "c(person(given = \"Joseph N\",\"Paulson\",email =\n\"paulson.joseph@gene.com\",role = c(\"aut\", \"cre\")),\nperson(\"Cho-Yi\",\"Chen\",role=\"aut\"),\nperson(\"Camila\",\"Lopes-Ramos\",role=\"aut\"),\nperson(\"Marieke\",\"Kuijjer\",role=\"aut\"),\nperson(\"John\",\"Platig\",role=\"aut\"),\nperson(\"Abhijeet\",\"Sonawane\",role=\"aut\"),\nperson(\"Maud\",\"Fagny\",role=\"aut\"),\nperson(\"Kimberly\",\"Glass\",role=\"aut\"),\nperson(\"John\",\"Quackenbush\",email =\n\"johnq@jimmy.harvard.edu\",role=\"aut\"))", "Description": "Expedite large RNA-Seq analyses using a combination of\npreviously developed tools. YARN is meant to make it easier for\nthe user in performing basic mis-annotation quality control,\nfiltering, and condition-aware normalization. YARN leverages\nmany Bioconductor tools and statistical techniques to account\nfor the large heterogeneity and sparsity found in very large\nRNA-seq experiments.", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "biocViews": "Software, QualityControl, GeneExpression, Sequencing,\nPreprocessing, Normalization, Annotation, Visualization,\nClustering", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:44:40 UTC", "RemoteUrl": "https://github.com/bioc/yarn", "RemoteRef": "RELEASE_3_23", "RemoteSha": "ca31e739d8f3745bcf097133f294000ee6415afb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:31:11 UTC", "User": "root" }, "Author": "Joseph N Paulson [aut, cre],\nCho-Yi Chen [aut],\nCamila Lopes-Ramos [aut],\nMarieke Kuijjer [aut],\nJohn Platig [aut],\nAbhijeet Sonawane [aut],\nMaud Fagny [aut],\nKimberly Glass [aut],\nJohn Quackenbush [aut]", "Maintainer": "Joseph N Paulson ", "MD5sum": "1015fb6c58385c04128ab819267bea95", "_user": "bioc-release", "_type": "src", "_file": "yarn_1.38.0.tar.gz", "_fileid": "e16e3e11459c6b7975dc4b994275e19bf4cf3e69fd81afcef9f64537314263ae", "_filesize": 3597190, "_sha256": "e16e3e11459c6b7975dc4b994275e19bf4cf3e69fd81afcef9f64537314263ae", "_created": "2026-05-30T10:31:11.000Z", "_published": "2026-05-30T15:37:56.874Z", "_jobs": [ { "job": 78642840095, "time": 197, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307659796" }, { "job": 78642840120, "time": 506, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307689045" }, { "job": 78642840103, "time": 461, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7307684898" }, { "job": 78642840117, "time": 322, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7309307288" }, { "job": 78642840109, "time": 252, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7309298503" }, { "job": 78640724757, "time": 347, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307532627" }, { "job": 78642840086, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307656041" }, { "job": 78642840121, "time": 393, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7307678181" }, { "job": 78642840108, "time": 355, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7307674349" }, { "job": 78642840123, "time": 374, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7307676274" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/yarn", "_commit": { "id": "ca31e739d8f3745bcf097133f294000ee6415afb", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380280 }, "_maintainer": { "name": "Joseph N Paulson", "email": "paulson.joseph@gene.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Biobase", "role": "Depends" }, { "package": "biomaRt", "role": "Imports" }, { "package": "downloader", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "preprocessCore", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "quantro", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 0.8", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.39.0", "bioc": "3.24" }, { "branch": "release", "version": "1.38.0", "bioc": "3.23" } ], "_topics": [ "software", "qualitycontrol", "geneexpression", "sequencing", "preprocessing", "normalization", "annotation", "visualization", "clustering" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 568, "source": "https://www.bioconductor.org/packages/stats/bioc/yarn" }, "_searchresults": 33, "_rbuild": "4.6.0", "_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/yarn.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "annotateFromBiomart", "checkMisAnnotation", "checkTissuesToMerge", "downloadGTEx", "filterGenes", "filterLowGenes", "filterMissingGenes", "filterSamples", "normalizeTissueAware", "plotCMDS", "plotDensity", "plotHeatmap" ], "_datasets": [ { "name": "bladder", "title": "Bladder RNA-seq data from the GTEx consortium", "object": "bladder", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false }, { "name": "skin", "title": "Skin RNA-seq data from the GTEx consortium", "object": "skin", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "annotateFromBiomart", "title": "Annotate your Expression Set with biomaRt", "topics": [ "annotateFromBiomart" ] }, { "page": "bladder", "title": "Bladder RNA-seq data from the GTEx consortium", "topics": [ "bladder" ] }, { "page": "checkMisAnnotation", "title": "Check for wrong annotation of a sample using classical MDS and control genes.", "topics": [ "checkMisAnnotation" ] }, { "page": "checkTissuesToMerge", "title": "Check tissues to merge based on gene expression profile", "topics": [ "checkTissuesToMerge" ] }, { "page": "downloadGTEx", "title": "Download GTEx files and turn them into ExpressionSet object", "topics": [ "downloadGTEx" ] }, { "page": "extractMatrix", "title": "Extract the appropriate matrix", "topics": [ "extractMatrix" ] }, { "page": "filterGenes", "title": "Filter specific genes", "topics": [ "filterGenes" ] }, { "page": "filterLowGenes", "title": "Filter genes that have less than a minimum threshold CPM for a given group/tissue", "topics": [ "filterLowGenes" ] }, { "page": "filterMissingGenes", "title": "Filter genes not expressed in any sample", "topics": [ "filterMissingGenes" ] }, { "page": "filterSamples", "title": "Filter samples", "topics": [ "filterSamples" ] }, { "page": "normalizeTissueAware", "title": "Normalize in a tissue aware context", "topics": [ "normalizeTissueAware" ] }, { "page": "plotCMDS", "title": "Plot classical MDS of dataset", "topics": [ "plotCMDS" ] }, { "page": "plotDensity", "title": "Density plots of columns in a matrix", "topics": [ "plotDensity" ] }, { "page": "plotHeatmap", "title": "Plot heatmap of most variable genes", "topics": [ "plotHeatmap" ] }, { "page": "qsmooth", "title": "Quantile shrinkage normalization", "topics": [ "qsmooth" ] }, { "page": "qstats", "title": "Compute quantile statistics", "topics": [ "qstats" ] }, { "page": "skin", "title": "Skin RNA-seq data from the GTEx consortium", "topics": [ "skin" ] } ], "_readme": "https://github.com/bioc/yarn/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64", "beanplot", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "bumphunter", "cachem", "caTools", "cigarillo", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "digest", "dir.expiry", "doParallel", "doRNG", "downloader", "dplyr", "edgeR", "farver", "fastmap", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GEOquery", "ggplot2", "glue", "gplots", "gtable", "gtools", "h5mread", "HDF5Array", "hms", "httr", "httr2", "illuminaio", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mime", "minfi", "multtest", "nlme", "nor1mix", "openssl", "pillar", "pkgconfig", "plyr", "png", "preprocessCore", "prettyunits", "progress", "purrr", "quadprog", "quantro", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "readr", "rentrez", "reshape", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rngtools", "Rsamtools", "RSQLite", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "scales", "scrime", "selectr", "Seqinfo", "siggenes", "snow", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "XML", "xml2", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "yarn.Rmd", "filename": "yarn.html", "title": "YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization", "author": "Joseph N. Paulson & John Quackenbush", "engine": "knitr::rmarkdown", "headings": [ "YARN - Yet Another RNa-seq package", "Installation", "Quick Introduction", "Preprocessing", "Helper functions", "Information" ], "created": "2016-10-17 09:38:00", "modified": "2018-08-30 17:58:23", "commits": 2 } ], "_score": 4.518513939877888, "_indexed": false, "_nocasepkg": "yarn", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/yarn", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.38.0", "date": "2026-05-30T10:54:26.000Z", "distro": "noble", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "c9ebfdf44ef8aade08af49d3356131bfad0761638fd9aa3774a9d22176486ab5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.6.0", "os": "linux", "version": "1.38.0", "date": "2026-05-30T10:53:37.000Z", "distro": "noble", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "56771fbea5de7f86be2043313963f81cf4ed484d4ce2d8257c7e334da3db8bbd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.5.3", "os": "mac", "version": "1.38.0", "date": "2026-05-30T15:33:41.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "a478135f3aefa01c4ba86fd6d382ef3347f2aea98e91da004fdbc11b5680639e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.6.0", "os": "mac", "version": "1.38.0", "date": "2026-05-30T15:33:30.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "74636cb1c845906d72420559bb678c43fd050a70fdc88f401dc76e96bbed579c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.6.0", "os": "wasm", "version": "1.38.0", "date": "2026-05-30T10:53:02.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "f5d7e2f4b8210a20b54b578437e93ab1c7314a63372a55686b1b2d9fcc6a9ae9", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.7.0", "os": "win", "version": "1.38.0", "date": "2026-05-30T10:52:02.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "1790a8f62550c46d4e59d4dd8935a55f46e664f98f024ef85dd85d9161c67a52", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.5.3", "os": "win", "version": "1.38.0", "date": "2026-05-30T10:51:39.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "7fddfa204e6f8b0b42bacc4355268782d4acf1231e9f13f8b9135070c83d7060", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" }, { "r": "4.6.0", "os": "win", "version": "1.38.0", "date": "2026-05-30T10:52:00.000Z", "commit": "ca31e739d8f3745bcf097133f294000ee6415afb", "fileid": "e31c5f9d83ff3755e91b351581506c3647ed493ddb581093da13be11c0045cb1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26680414633" } ] }