{ "_id": "6ac0d57191601a2ad29995f2", "Package": "BEAT", "Type": "Package", "Version": "1.51.0", "Title": "BEAT - BS-Seq Epimutation Analysis Toolkit", "Date": "2014-02-14", "Maintainer": "Kemal Akman ", "Author": "Kemal Akman ", "Description": "Model-based analysis of single-cell methylation data", "License": "LGPL (>= 3.0)", "Packaged": { "Date": "2026-10-03 10:07:33 UTC", "User": "root" }, "biocViews": "ImmunoOncology, Genetics, MethylSeq, Software,\nDNAMethylation, Epigenetics", "Config/pak/sysreqs": "make libbz2-dev libjpeg-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:33 UTC", "RemoteUrl": "https://github.com/bioc/BEAT", "RemoteRef": "HEAD", "RemoteSha": "6c3988d029ea74187e52199fbf6130eb13938d5b", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "BEAT_1.51.0.tar.gz", "_fileid": "https://r2.ropensci.org/a1d7eaac055ff1159e5c10c7d7ff90a819c98a8aae6c853bd2b75d319eb090df", "_filesize": 3495628, "_sha256": "a1d7eaac055ff1159e5c10c7d7ff90a819c98a8aae6c853bd2b75d319eb090df", "_expires": "2027-01-11T10:14:07.000Z", "_created": "2026-10-03T10:07:33.000Z", "_published": "2026-10-03T10:14:09.696Z", "_bioccheck": { "error": 1, "warning": 6, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519", "_status": "success", "_upstream": "https://github.com/bioc/BEAT", "_commit": { "id": "6c3988d029ea74187e52199fbf6130eb13938d5b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379913 }, "_maintainer": { "name": "Kemal Akman", "email": "akman@mpipz.mpg.de" }, "_distro": "resolute", "_jobs": [ { "job": 111181125377, "time": 168, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11270974775" }, { "job": 111181125398, "time": 340, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11270638770" }, { "job": 111181125457, "time": 323, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11271294537" }, { "job": 111181125368, "time": 216, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11270643856" }, { "job": 111181125420, "time": 208, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11271378924" }, { "job": 111180437465, "time": 249, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11271244112" }, { "job": 111181125407, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11271515163" }, { "job": 111181125432, "time": 240, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11271705082" }, { "job": 111181125436, "time": 231, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11270433947" }, { "job": 111181125425, "time": 221, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11270748665" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.0", "role": "Depends" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "ShortRead", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "genetics", "methylseq", "software", "dnamethylation", "epigenetics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 470, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 648, "source": "https://www.bioconductor.org/packages/stats/bioc/BEAT" }, "_mentions": 54, "_searchresults": 9, "_rbuild": "4.6.1", "_assets": [ "extra/BEAT.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "epimutation_calls", "generate_results", "makeParams", "positions_to_regions" ], "_datasets": [ { "name": "positions", "title": "Sample dataset of CpG positions for a single cell BS-seq sample", "object": "BEAT", "file": "BEAT.RData", "class": [ "data.frame" ], "fields": [ "chr", "pos", "meth", "unmeth" ], "rows": 235935, "table": true, "tojson": true }, { "name": "positions.reference", "title": "Sample dataset of CpG positions for a reference BS-Seq sample", "object": "BEAT", "file": "BEAT.RData", "class": [ "data.frame" ], "fields": [ "chr", "pos", "meth", "unmeth" ], "rows": 237531, "table": true, "tojson": true } ], "_help": [ { "page": "BEAT", "title": "BEAT - BS-Seq Epimutation Analysis Toolkit", "topics": [ "BEAT-package", "BEAT" ] }, { "page": "epimutation_calls", "title": "Returns epimutation rates and sites.", "topics": [ "epimutation_calls" ] }, { "page": "generate_results", "title": "Computes model methylation states for genomic region counts of a list of samples.", "topics": [ "generate_results" ] }, { "page": "makeParams", "title": "Creates a parameter object of arguments to be used with other BEAT functions.", "topics": [ "makeParams" ] }, { "page": "positions", "title": "Sample dataset of CpG positions for a single cell BS-seq sample", "topics": [ "positions" ] }, { "page": "positions_to_regions", "title": "Converts methylation counts for single genomic positions to counts for genomic regions", "topics": [ "positions_to_regions" ] }, { "page": "positions.reference", "title": "Sample dataset of CpG positions for a reference BS-Seq sample", "topics": [ "positions.reference" ] } ], "_rundeps": [ "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "BSgenome", "cigarillo", "codetools", "cpp11", "crayon", "curl", "deldir", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "httr", "hwriter", "interp", "IRanges", "jpeg", "jsonlite", "lambda.r", "lattice", "latticeExtra", "MASS", "matrixStats", "mime", "openssl", "png", "pwalign", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "Rsamtools", "rtracklayer", "S4Vectors", "Seqinfo", "ShortRead", "snow", "sys", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "BEAT.Rnw", "filename": "BEAT.pdf", "title": "Analysing single-cell BS-Seq data with the \"BEAT\" package", "engine": "utils::Sweave", "headings": [], "created": "2014-02-12 19:47:01", "modified": "2014-02-12 19:47:01", "commits": 1 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "beat", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.51.0", "date": "2026-10-03T10:10:52.000Z", "distro": "resolute", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/c86ba43205895f84549e1c1cb901d602b42ace4ad1ebbf8abae4c7cd1585ca82", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.6.1", "os": "linux", "version": "1.51.0", "date": "2026-10-03T10:10:49.000Z", "distro": "resolute", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/65222a9d8cfa10cffb92164bbf25b9107735bbe5e438e072fcc2aad96ac01f41", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-10-03T10:09:28.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/ba867fac740b200bd1dbd9d98137dc9d874e5d3f70677d3ddce98cc936b6a989", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.6.1", "os": "mac", "version": "1.51.0", "date": "2026-10-03T10:09:38.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/f15399bab19a93314d0da7342807f31385e7b9fc13d9e829ed0bddda1dee12fa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.6.0", "os": "wasm", "version": "1.51.0", "date": "2026-10-03T10:10:10.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/2ea7e239a49cb97f5b6e80c555dec8ac8ac27314e6fc72032b91a870ad34a952", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.7.0", "os": "win", "version": "1.51.0", "date": "2026-10-03T10:09:06.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/e356bedff826d335c151f7cd2e08458adb0390bbe470ed699b4c2dd4afd5ac03", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-10-03T10:09:06.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/56d19b1d86fe5e80af39cc40dc5b9af1a43287cc836a7532b77ba5b8066a744f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" }, { "r": "4.6.1", "os": "win", "version": "1.51.0", "date": "2026-10-03T10:09:18.000Z", "commit": "6c3988d029ea74187e52199fbf6130eb13938d5b", "fileid": "https://r2.ropensci.org/524ceddda3d41e55b06f7a12c3ca98842b241853c07e530a5efa2c48c2d8f67a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37115134519" } ] }