{ "_id": "6a1ab6061d7bb097a09d5dbe", "Package": "prebs", "Title": "Probe region expression estimation for RNA-seq data for improved\nmicroarray comparability", "Description": "The prebs package aims at making RNA-sequencing (RNA-seq)\ndata more comparable to microarray data. The comparability is\nachieved by summarizing sequencing-based expressions of probe\nregions using a modified version of RMA algorithm. The pipeline\ntakes mapped reads in BAM format as an input and produces\neither gene expressions or original microarray probe set\nexpressions as an output.", "Version": "1.53.0", "Author": "Karolis Uziela and Antti Honkela", "Maintainer": "Karolis Uziela ", "License": "Artistic-2.0", "Collate": "'PREBS.R'", "biocViews": "ImmunoOncology, Microarray, RNASeq, Sequencing,\nGeneExpression, Preprocessing", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libuv1-dev libxml2-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:37:38 UTC", "RemoteUrl": "https://github.com/bioc/prebs", "RemoteRef": "HEAD", "RemoteSha": "8cab52a03a5a05132ebda14c36b995009d18dee6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:09:07 UTC", "User": "root" }, "MD5sum": "e3de55fe024fe5395e99c9989661332a", "_user": "bioc", "_type": "src", "_file": "prebs_1.53.0.tar.gz", "_fileid": "7d8d49621cec62859fb715e5e7a0049ef42e0745cc6434016f91401ceba1b629", "_filesize": 226856, "_sha256": "7d8d49621cec62859fb715e5e7a0049ef42e0745cc6434016f91401ceba1b629", "_created": "2026-05-30T07:09:07.000Z", "_published": "2026-05-30T10:03:50.969Z", "_jobs": [ { "job": 78632511451, "time": 200, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306363548" }, { "job": 78632511459, "time": 499, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306399203" }, { "job": 78632511468, "time": 509, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306400310" }, { "job": 78632511452, "time": 255, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307243905" }, { "job": 78632511467, "time": 322, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307257297" }, { "job": 78632169691, "time": 369, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306340401" }, { "job": 78632511466, "time": 154, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306358328" }, { "job": 78632511474, "time": 681, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306419893" }, { "job": 78632511473, "time": 799, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306432529" }, { "job": 78632511475, "time": 708, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306422927" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/prebs", "_commit": { "id": "8cab52a03a5a05132ebda14c36b995009d18dee6", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379858 }, "_maintainer": { "name": "Karolis Uziela", "email": "karolis.uziela@scilifelab.se", "login": "uziela", "description": "", "uuid": 3288367 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.14.0", "role": "Depends" }, { "package": "GenomicAlignments", "role": "Depends" }, { "package": "affy", "role": "Depends" }, { "package": "RPA", "role": "Depends" }, { "package": "parallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.13.3", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "prebsdata", "role": "Suggests" }, { "package": "hgu133plus2cdf", "role": "Suggests" }, { "package": "hgu133plus2probe", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "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": [ "immunooncology", "microarray", "rnaseq", "sequencing", "geneexpression", "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 417, "source": "https://www.bioconductor.org/packages/stats/bioc/prebs" }, "_mentions": 1, "_searchresults": 9, "_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/prebs.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calc_prebs" ], "_help": [ { "page": "calc_prebs", "title": "Calculate PREBS values", "topics": [ "calc_prebs" ] }, { "page": "prebs", "title": "PREBS package", "topics": [ "prebs-package", "prebs" ] } ], "_rundeps": [ "abind", "ade4", "affy", "affyio", "ape", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocManager", "BiocParallel", "BiocStyle", "biomformat", "Biostrings", "bitops", "bookdown", "bslib", "cachem", "cigarillo", "cli", "cluster", "codetools", "cpp11", "crayon", "data.table", "DelayedArray", "digest", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "multtest", "nlme", "permute", "phyloseq", "pixmap", "pkgconfig", "plyr", "preprocessCore", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "Rhtslib", "rlang", "rmarkdown", "RPA", "Rsamtools", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "sp", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "tinytex", "vctrs", "vegan", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "prebs.Rnw", "filename": "prebs.pdf", "title": "prebs User Guide", "engine": "utils::Sweave", "headings": [], "created": "2013-04-02 00:04:28", "modified": "2018-09-06 23:18:24", "commits": 10 } ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "prebs", "_universes": [ "bioc", "uziela" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.53.0", "date": "2026-05-30T07:13:00.000Z", "distro": "noble", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "ae8b22d927c99da9ae54a347300a19dbaff6cbcd02f67ded911332aee5a224b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.6.0", "os": "linux", "version": "1.53.0", "date": "2026-05-30T07:13:26.000Z", "distro": "noble", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "d5ff6579f3418f336697f3eb723f644ca13f532e78f5d76431013c7c766c9ce4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.5.3", "os": "mac", "version": "1.53.0", "date": "2026-05-30T09:37:05.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "61cd31b2519adeaf2f3f0526c77f953bdd0264b1c8f0e2fbb96c77430036e426", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.6.0", "os": "mac", "version": "1.53.0", "date": "2026-05-30T09:38:37.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "32ce57b92925e93d2ec97e45ad2a44795825d76fc5009b1f035b6b879064c79f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.6.0", "os": "wasm", "version": "1.53.0", "date": "2026-05-30T07:12:18.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "3334baf65502188d898a9458d89977dfe8f3748e1b19c878667ffe8bc5a3461c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.7.0", "os": "win", "version": "1.53.0", "date": "2026-05-30T07:14:55.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "b68f77050141e5013f0b05f66d5140e5fa0e76775fa72b00406fa2760421b22d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.5.3", "os": "win", "version": "1.53.0", "date": "2026-05-30T07:15:20.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "22af9850fe40338b8dcde421fa352116fc39201f932a7289b96320eb4e0406b9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" }, { "r": "4.6.0", "os": "win", "version": "1.53.0", "date": "2026-05-30T07:14:20.000Z", "commit": "8cab52a03a5a05132ebda14c36b995009d18dee6", "fileid": "c0039c75108f3810a0b7d109c9424ea377214f8c0f48af82238e64a071fc7d0f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677578610" } ] }