{ "_id": "6ae7564a9ceaa78f20099ddf", "Package": "altcdfenvs", "Version": "2.75.0", "Title": "alternative CDF environments (aka probeset mappings)", "Author": "Laurent Gautier ", "Maintainer": "Laurent Gautier ", "biocViews": "Microarray, OneChannel, QualityControl, Preprocessing,\nAnnotation, ProprietaryPlatforms, Transcription", "Description": "Convenience data structures and functions to handle\ncdfenvs", "License": "GPL (>= 2)", "Collate": "appendCdfEnvAffy.R buildCdfEnv.matchprobes.R\nbuildCdfEnv.biostrings.R CdfEnv.R cdfenvs.R copyCdfEnvAffy.R\nreadFASTA.R removeIndex.R unique.CdfEnvAffy.R", "LazyLoad": "yes", "Packaged": { "Date": "2026-11-01 13:22:03 UTC", "User": "root" }, "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:30:30 UTC", "RemoteUrl": "https://github.com/bioc/altcdfenvs", "RemoteRef": "HEAD", "RemoteSha": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "altcdfenvs_2.75.0.tar.gz", "_fileid": "https://r2.ropensci.org/ade04ef35e9eb95183309afbf77b06997ec792b146a06b13ee43a568c2854645", "_filesize": 472667, "_sha256": "ade04ef35e9eb95183309afbf77b06997ec792b146a06b13ee43a568c2854645", "_expires": "2027-02-09T15:10:00.000Z", "_created": "2026-11-01T13:22:03.000Z", "_published": "2026-11-01T15:10:02.473Z", "_upstream": "https://github.com/bioc/altcdfenvs", "_status": "success", "_maintainer": { "name": "Laurent Gautier", "email": "lgautier@gmail.com", "login": "lgautier", "description": "Data Science, Life Sciences & Healthcare", "uuid": 650866 }, "_jobs": [ { "job": 124861019761, "time": 202, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13085673158" }, { "job": 124861019854, "time": 236, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13085929159" }, { "job": 124861019825, "time": 321, "config": "linux-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13085919512" }, { "job": 124861019731, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "13088379350" }, { "job": 124861019748, "time": 184, "config": "macos-release-arm64", "r": "4.6.2", "check": "NOTE", "artifact": "13088538320" }, { "job": 124857787655, "time": 304, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13085073660" }, { "job": 124861019818, "time": 159, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13086198448" }, { "job": 124861019777, "time": 502, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "13085831142" }, { "job": 124861019872, "time": 473, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "13085747162" }, { "job": 124861019807, "time": 455, "config": "windows-release-x86_64", "r": "4.6.2", "check": "NOTE", "artifact": "13086395401" } ], "_bioccheck": { "error": 2, "warning": 5, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362", "_commit": { "id": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379430 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.7", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocGenerics", "version": ">= 0.1.0", "role": "Depends" }, { "package": "S4Vectors", "version": ">= 0.9.25", "role": "Depends" }, { "package": "Biobase", "version": ">= 2.15.1", "role": "Depends" }, { "package": "affy", "role": "Depends" }, { "package": "makecdfenv", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "hypergraph", "role": "Depends" }, { "package": "plasmodiumanophelescdf", "role": "Suggests" }, { "package": "hgu95acdf", "role": "Suggests" }, { "package": "hgu133aprobe", "role": "Suggests" }, { "package": "hgu133a.db", "role": "Suggests" }, { "package": "hgu133acdf", "role": "Suggests" }, { "package": "Rgraphviz", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.75.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "2.74.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microarray", "onechannel", "qualitycontrol", "preprocessing", "annotation", "proprietaryplatforms", "transcription" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 777, "source": "https://www.bioconductor.org/packages/stats/bioc/altcdfenvs" }, "_mentions": 5, "_searchresults": 8, "_abi": { "exports": [ { "key": "altcdfenvs::AffyProbesMatch", "hash": "c89e6da0905fcf0a" }, { "key": "altcdfenvs::CdfEnvAffy", "hash": "82856be459d8861f" }, { "key": "altcdfenvs::generic:index2xy", "hash": "4f707d48a52fc9a1" }, { "key": "altcdfenvs::generic:toHypergraph", "hash": "9b1640c77475f816" }, { "key": "altcdfenvs::generic:xy2index", "hash": "7f7e8b20af37b8c4" } ], "imports": [ { "key": "BiocGenerics::generic:combine", "hash": "ee9c69fbcf551ee0" }, { "key": "affy::generic:geneNames", "hash": "ea2ef1acba571f83" }, { "key": "affy::generic:indexProbes", "hash": "6d54bc3c13dfeb11" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/altcdfenvs.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "appendCdfEnvAffy", "buildCdfEnv.biostrings", "buildCdfEnv.matchprobes", "copyCdfEnvAffy", "countduplicated", "countskip.FASTA.entries", "geneNames.CdfEnvAffy", "getCdfEnvAffy", "getxy.probeseq", "grep.FASTA.entry", "index2xy", "index2xy.CdfEnvAffy", "indexProbes.CdfEnvAffy", "matchAffyProbes", "mmProbes", "plot.CdfEnvAffy", "print.FASTA", "printValidCdfEnvAffy", "read.FASTA.entry", "read.n.FASTA.entries", "read.n.FASTA.entries.split", "read.n.FASTA.headers", "read.n.FASTA.sequences", "removeIndex", "skip.FASTA.entry", "toHypergraph", "unique.CdfEnvAffy", "validAffyBatch", "validCdfEnvAffy", "wrapCdfEnvAffy", "write.FASTA", "xy2index", "xy2index.CdfEnvAffy" ], "_datasets": [ { "name": "cdfenvEx", "title": "CdfEnvAffy", "object": "cdfenvEx", "file": "cdfenvEx.rda", "class": [ "CdfEnvAffy" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "AffyProbesMatch-class", "title": "Class \"AffyProbesMatch\"", "topics": [ "AffyProbesMatch-class", "combine,AffyProbesMatch,AffyProbesMatch-method", "show,AffyProbesMatch-method", "toHypergraph,AffyProbesMatch-method" ] }, { "page": "appendCdfEnvAffy", "title": "append probe sets to a CdfEnvAffy", "topics": [ "appendCdfEnvAffy" ] }, { "page": "buildCdfEnv.biostrings", "title": "Build CDF environments", "topics": [ "buildCdfEnv.biostrings" ] }, { "page": "CdfEnvAffy-class", "title": "Class \"CdfEnvAffy\"", "topics": [ "CdfEnvAffy-class", "coerce,CdfEnvAffy,Cdf-method", "coerce,CdfEnvAffy,environment-method", "geneNames,CdfEnvAffy-method", "index2xy,CdfEnvAffy-method", "indexProbes,CdfEnvAffy,character-method", "plot,CdfEnvAffy,missing-method", "show,CdfEnvAffy-method", "toHypergraph,CdfEnvAffy-method", "xy2index,CdfEnvAffy-method", "[,CdfEnvAffy,character,missing,missing-method" ] }, { "page": "cdfenvEx", "title": "CdfEnvAffy", "topics": [ "cdfenvEx" ] }, { "page": "cdfenv", "title": "functions related to cdfenvs", "topics": [ "buildCdfEnv.matchprobes", "CdfEnv", "getCdfEnvAffy", "wrapCdfEnvAffy" ] }, { "page": "copyCdfEnvAffy", "title": "make a copy of a CdfEnvAffy", "topics": [ "copyCdfEnvAffy" ] }, { "page": "countduplicated", "title": "Count the number of times probes are used", "topics": [ "countduplicated" ] }, { "page": "geneNames", "title": "get the names of the known probe sets", "topics": [ "geneNames.CdfEnvAffy" ] }, { "page": "getxy.probeseq", "title": "A function to get the XY coordinates from a probes sequences data frame", "topics": [ "getxy.probeseq" ] }, { "page": "index2xy", "title": "Functions to shuttle from indexes to XY coordinates", "topics": [ "index2xy", "index2xy.CdfEnvAffy", "xy2index", "xy2index.CdfEnvAffy" ] }, { "page": "indexProbes.CdfEnvAffy", "title": "indexes for probes", "topics": [ "indexProbes.CdfEnvAffy" ] }, { "page": "matchAffyProbes", "title": "Match the probes on an Affymetrix array", "topics": [ "matchAffyProbes", "mmProbes" ] }, { "page": "plot.CdfEnvAffy", "title": "A function to `plot' a CdfEnvAffy", "topics": [ "plot.CdfEnvAffy" ] }, { "page": "utils.FASTA", "title": "Functions to work with FASTA files / connections", "topics": [ "countskip.FASTA.entries", "grep.FASTA.entry", "print.FASTA", "read.FASTA.entry", "read.n.FASTA.entries", "read.n.FASTA.entries.split", "read.n.FASTA.headers", "read.n.FASTA.sequences", "skip.FASTA.entry", "write.FASTA" ] }, { "page": "removeIndex", "title": "A function to remove probes in an environment", "topics": [ "removeIndex" ] }, { "page": "toHypergraph", "title": "Transform to an hypergraph", "topics": [ "toHypergraph" ] }, { "page": "unique.CdfEnvAffy", "title": "Remove duplicated elements from a CdfEnvAffy", "topics": [ "unique.CdfEnvAffy" ] }, { "page": "validAffyBatch", "title": "Check validity of a CdfEnvAffy.", "topics": [ "printValidCdfEnvAffy", "validAffyBatch", "validCdfEnvAffy" ] } ], "_rundeps": [ "affy", "affyio", "Biobase", "BiocGenerics", "BiocManager", "Biostrings", "crayon", "generics", "graph", "hypergraph", "IRanges", "makecdfenv", "preprocessCore", "S4Vectors", "Seqinfo", "XVector" ], "_vignettes": [ { "source": "altcdfenvs.Rnw", "filename": "altcdfenvs.pdf", "title": "altcdfenvs", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:51:00", "modified": "2013-11-01 19:51:00", "commits": 1 }, { "source": "ngenomeschips.Rnw", "filename": "ngenomeschips.pdf", "title": "Alternative CDF environments for 2(or more)-genomes chips", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:51:00", "modified": "2019-02-25 12:57:32", "commits": 2 }, { "source": "modify.Rnw", "filename": "modify.pdf", "title": "Modifying existing CDF environments to make alternative CDF environments", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 19:51:00", "modified": "2019-02-25 12:57:32", "commits": 2 } ], "_score": 4.477121254719663, "_indexed": true, "_nocasepkg": "altcdfenvs", "_universes": [ "bioc", "lgautier" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.75.0", "date": "2026-11-01T13:54:09.000Z", "distro": "resolute", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/c80c0ec9b5c95c3fb826dd7cc5c00b80362025b2a506f82402caa12ed3ebb5ad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.6.2", "os": "linux", "version": "2.75.0", "date": "2026-11-01T13:55:09.000Z", "distro": "resolute", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/8924356574be625873041331ffb821246042046ef1dd797405004a19d6285244", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.5.3", "os": "mac", "version": "2.75.0", "date": "2026-11-01T15:08:32.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/59c83ea38890e0753c6f8ac85512cfe2a08ceb9524a55c1d21e3c85caede5092", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.6.2", "os": "mac", "version": "2.75.0", "date": "2026-11-01T15:08:33.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/fe9cd35327b84ac10de2cd689fb6cdbc2b0842f0a297d03a827bd6700c23e154", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.6.0", "os": "wasm", "version": "2.75.0", "date": "2026-11-01T13:53:36.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/b5021f5e4a19002eaa43f3818f68c3df176e0b96bd2518d5588aa88f4fa0bd36", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.7.0", "os": "win", "version": "2.75.0", "date": "2026-11-01T13:37:37.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/063ae7cea8bddfab7d226714305087d96facd92958599ba982bc913c387011af", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.5.3", "os": "win", "version": "2.75.0", "date": "2026-11-01T13:37:14.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/1e13f37ba0458658574013d0d68d6dce4f6bc3d316b00906d24a2da7108060fa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" }, { "r": "4.6.2", "os": "win", "version": "2.75.0", "date": "2026-11-01T13:37:11.000Z", "commit": "9f56b80bdbe5b699507c768dd8b4431cf82e43d1", "fileid": "https://r2.ropensci.org/25f20fc6d88f2b0756d58484a30358e38d3a0dde4858966c2af73b32c47a9a4e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309308362" } ] }