{ "_id": "6a49753e424221e3da02e903", "Package": "gcrma", "Title": "Background Adjustment Using Sequence Information", "Version": "2.85.0", "Author": "Jean(ZHIJIN) Wu, Rafael Irizarry with contributions from James\nMacDonald Jeff Gentry", "Description": "Background adjustment using sequence information", "Maintainer": "Z. Wu ", "License": "LGPL", "biocViews": "Microarray, OneChannel, Preprocessing", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:30:11 UTC", "RemoteUrl": "https://github.com/bioc/gcrma", "RemoteRef": "HEAD", "RemoteSha": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-23 15:27:19 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "gcrma_2.85.0.tar.gz", "_fileid": "https://r2.ropensci.org/30aa6d80e2ad9e60c34884827838009a90e1c5e2b4cc56809924d425651a432c", "_filesize": 275745, "_sha256": "30aa6d80e2ad9e60c34884827838009a90e1c5e2b4cc56809924d425651a432c", "_expires": "2026-10-12T21:03:57.000Z", "_created": "2026-06-23T15:27:19.000Z", "_published": "2026-07-04T21:03:58.948Z", "_bioccheck": { "error": 3, "warning": 5, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716", "_status": "success", "_upstream": "https://github.com/bioc/gcrma", "_commit": { "id": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379411 }, "_maintainer": { "name": "Z. Wu", "email": "zwu@stat.brown.edu" }, "_distro": "resolute", "_jobs": [ { "job": 85166840695, "time": 227, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7825511287" }, { "job": 85166840802, "time": 211, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7825504981" }, { "job": 85166840800, "time": 274, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7825531381" }, { "job": 85166840928, "time": 191, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7825495920" }, { "job": 85166840777, "time": 259, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7825525091" }, { "job": 85166840954, "time": 237, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7825498749" }, { "job": 85166840803, "time": 251, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7825513297" }, { "job": 85166840796, "time": 167, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7825485376" }, { "job": 85166840818, "time": 259, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7825525445" }, { "job": 85166840645, "time": 244, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7825406042" }, { "job": 85166840869, "time": 238, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7825515867" }, { "job": 85166840671, "time": 502, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7825632022" }, { "job": 85166840697, "time": 512, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7825635432" }, { "job": 85166840683, "time": 475, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7825619902" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.6.0", "role": "Depends" }, { "package": "affy", "version": ">= 1.23.2", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "affy", "version": ">= 1.23.2", "role": "Imports" }, { "package": "affyio", "version": ">= 1.13.3", "role": "Imports" }, { "package": "XVector", "role": "Imports" }, { "package": "Biostrings", "version": ">= 2.11.32", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "affydata", "role": "Suggests" }, { "package": "tools", "role": "Suggests" }, { "package": "splines", "role": "Suggests" }, { "package": "hgu95av2cdf", "role": "Suggests" }, { "package": "hgu95av2probe", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 11, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.85.0", "bioc": "3.24" }, { "branch": "release", "version": "2.84.0", "bioc": "3.23" } ], "_topics": [ "microarray", "onechannel", "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 186, "_searchresults": 198, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gcrma.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "average.for.PAV", "base.profiles", "base.profiles.mm", "base.profiles.nc", "bg.adjust.affinities", "bg.adjust.constant", "bg.adjust.fullmodel", "bg.adjust.gcrma", "bg.adjust.mm", "bg.adjust.optical", "bg.parameters.ns", "check.probes", "compute.affinities", "compute.affinities.local", "compute.affinities2", "compute.affinity.coef", "fast.bkg", "gcrma", "gcrma.bg.transformation", "gcrma.bg.transformation.fast", "gcrma.engine", "gcrma.engine2", "getCDF", "getProbePackage", "GSB.adj", "just.gcrma", "justGCRMA", "left.sigma", "mem.bkg", "PAV", "plotBaseProfiles" ], "_datasets": [ { "name": "affinity.spline.coefs", "title": "Spline coefficients for estimation of affinity from probe sequence", "object": "affinity.spline.coefs", "file": "affinity.spline.coefs.rda", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "affinity.spline.coefs", "title": "Spline coefficients for estimation of affinity from probe sequence", "topics": [ "affinity.spline.coefs" ] }, { "page": "bg.adjust.affinities", "title": "Background adjustment with sequence information (internal function)", "topics": [ "bg.adjust.affinities", "bg.adjust.constant", "bg.adjust.fullmodel", "bg.adjust.mm", "bg.adjust.optical" ] }, { "page": "bg.adjust.gcrma", "title": "GCRMA background adjust (internal function)", "topics": [ "bg.adjust.gcrma" ] }, { "page": "bg.parameters.ns", "title": "Estimation of non-specific Binding Background Parameters", "topics": [ "average.for.PAV", "bg.parameters.ns", "left.sigma", "PAV" ] }, { "page": "compute.affinities", "title": "Probe Affinity computation", "topics": [ "base.profiles", "base.profiles.mm", "base.profiles.nc", "check.probes", "compute.affinities", "compute.affinities.local", "compute.affinities2", "compute.affinity.coef", "plotBaseProfiles" ] }, { "page": "gcrma", "title": "Robust Multi-Array expression measure using sequence information", "topics": [ "gcrma", "gcrma.bg.transformation", "gcrma.bg.transformation.fast", "GSB.adj" ] }, { "page": "gcrma.engine", "title": "GCRMA background adjust engine(internal function)", "topics": [ "gcrma.engine" ] }, { "page": "gcrma.engine2", "title": "GCRMA background adjust engine(internal function)", "topics": [ "gcrma.engine2" ] }, { "page": "justGCRMA", "title": "Compute GCRMA Directly from CEL Files", "topics": [ "just.gcrma", "justGCRMA" ] } ], "_rundeps": [ "affy", "affyio", "Biobase", "BiocGenerics", "BiocManager", "Biostrings", "crayon", "generics", "IRanges", "preprocessCore", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "gcrma2.0.Rnw", "filename": "gcrma2.0.pdf", "title": "gcrma1.2", "engine": "utils::Sweave", "headings": [ "Introduction", "What's new in version 2.0.0", "Options for gcrma", "Getting started: the simplest example", "More Examples with options", "Efficient use of gcrma" ], "created": "2013-11-01 19:49:25", "modified": "2013-11-01 19:49:25", "commits": 1 } ], "_score": 7.1162091258034, "_indexed": true, "_nocasepkg": "gcrma", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.85.0", "date": "2026-06-23T15:30:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/effda418292eed9f38bd17b2376ff7d11b8a5a3220afa1fa336faf680c6c0d49", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.7.0", "os": "linux", "version": "2.85.0", "date": "2026-06-23T15:31:25.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/9bbff7061a52eb967defabab164cb376e2a0dd001242dfbffd2fc6057cad48df", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "linux", "version": "2.85.0", "date": "2026-06-23T15:30:20.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/7818ff65d68ef855c0f9288283fe14cb5c79211efa81fe3d3f0acfeea5bc5c7d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "linux", "version": "2.85.0", "date": "2026-06-23T15:31:08.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/5d31fd3cf249ac1def87ae86b272607460334ebc4bc5ec0620869ddef3b3be15", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.5.3", "os": "mac", "version": "2.85.0", "date": "2026-06-23T15:29:59.000Z", "arch": "aarch64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/93277b070df6d394e6c0c33d29281fc6a578b58be2c7f586517797d4e66554c1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.5.3", "os": "mac", "version": "2.85.0", "date": "2026-06-23T15:30:15.000Z", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/5e92f082c46beebd34b1f25f52b11f64db650aa748c12ebaf9ec8198072a8b2b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "mac", "version": "2.85.0", "date": "2026-06-23T15:29:43.000Z", "arch": "aarch64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/06aab0ff27b29015bd8c982e7490449adf3b174d7b41ede97010bdfadc224041", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "mac", "version": "2.85.0", "date": "2026-06-23T15:30:29.000Z", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/f54cf494b3e892e270643a9eff39544c581834981c803c25173e25db183926f3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "wasm", "version": "2.85.0", "date": "2026-06-23T15:31:55.000Z", "arch": "emscripten", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/0ceb478f632c5fc5d91f2280bd12db28109f75c4afd2426ef4f2f877b8525a80", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.7.0", "os": "win", "version": "2.85.0", "date": "2026-06-23T15:35:07.000Z", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/79f239e7c190e4e809b1b3df00f2906688e2a60d4b381f10ed8ab74296c73c69", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.5.3", "os": "win", "version": "2.85.0", "date": "2026-06-23T15:35:01.000Z", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/68c56ae0667fd668d783a4c21b46eed972923447085fc7a8f17d8adab561a577", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" }, { "r": "4.6.0", "os": "win", "version": "2.85.0", "date": "2026-06-23T15:34:26.000Z", "arch": "x86_64", "commit": "b5a7b90c54064b337a8fed3d2fee94e15c613a77", "fileid": "https://r2.ropensci.org/f8a43938a8e53912fbcd5ef6598d7c9f6f407dd34f0722cd3642db69c9120999", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28036710716" } ] }