{ "_id": "6a2a60b97b7a29ca6003de52", "Package": "gcapc", "Title": "GC Aware Peak Caller", "Version": "1.36.0", "Author": "Mingxiang Teng and Rafael A. Irizarry", "Maintainer": "Mingxiang Teng ", "Description": "Peak calling for ChIP-seq data with consideration of\npotential GC bias in sequencing reads. GC bias is first\nestimated with generalized linear mixture models using\neffective GC strategy, then applied into peak significance\nestimation.", "VignetteBuilder": "knitr", "URL": "https://github.com/tengmx/gcapc", "License": "GPL-3", "biocViews": "Sequencing, ChIPSeq, BatchEffect, PeakDetection", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:44:47 UTC", "RemoteUrl": "https://github.com/bioc/gcapc", "RemoteRef": "RELEASE_3_23", "RemoteSha": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-11 07:03:38 UTC", "User": "root" }, "MD5sum": "513091e67468e7e63a0b25809da20fb9", "_user": "bioc-release", "_type": "src", "_file": "gcapc_1.36.0.tar.gz", "_fileid": "12873f874032a5aaea9fd8b0f00560c9814a0d6a55aba706479aea69b1773c99", "_filesize": 3906211, "_sha256": "12873f874032a5aaea9fd8b0f00560c9814a0d6a55aba706479aea69b1773c99", "_created": "2026-06-11T07:03:38.000Z", "_published": "2026-06-11T07:16:09.207Z", "_jobs": [ { "job": 80739619045, "time": 287, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7557156430" }, { "job": 80739619059, "time": 690, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7557279494" }, { "job": 80739619049, "time": 554, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7557238146" }, { "job": 80739619035, "time": 382, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7557243078" }, { "job": 80739619052, "time": 351, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7557220308" }, { "job": 80738423189, "time": 479, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7557071186" }, { "job": 80739619034, "time": 238, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7557142508" }, { "job": 80739619067, "time": 446, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7557206592" }, { "job": 80739619071, "time": 481, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7557216657" }, { "job": 80739619077, "time": 388, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7557188987" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/gcapc", "_commit": { "id": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "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": 1777380287 }, "_maintainer": { "name": "Mingxiang Teng", "email": "tengmx@gmail.com", "login": "tengmx", "description": "Bioinformatics", "uuid": 5973324 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "GenomicAlignments", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "chipseq", "batcheffect", "peakdetection" ], "_stars": 10, "_contributors": [ { "user": "tengmx", "count": 61, "uuid": 5973324 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 442, "source": "https://www.bioconductor.org/packages/stats/bioc/gcapc" }, "_devurl": "https://github.com/tengmx/gcapc", "_searchresults": 16, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/gcapc.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/tengmx/gcapc", "_realowner": "bioc", "_cranurl": false, "_exports": [ "bindWidth", "gcapcPeaks", "gcEffects", "peaksCAT", "read5endCoverage", "refinePeaks", "refineSites" ], "_help": [ { "page": "bindWidth", "title": "ChIP-seq Binding Width And Peak Window Size Estimation", "topics": [ "bindWidth" ] }, { "page": "gcapcPeaks", "title": "GC Effects Aware Peak Calling", "topics": [ "gcapcPeaks" ] }, { "page": "gcEffects", "title": "ChIP-seq GC Effects Estimation", "topics": [ "gcEffects" ] }, { "page": "peaksCAT", "title": "CATplot of Peaks", "topics": [ "peaksCAT" ] }, { "page": "read5endCoverage", "title": "Reads Coverage Using 5-end Base", "topics": [ "read5endCoverage" ] }, { "page": "refinePeaks", "title": "Refine Peaks with GC Effects", "topics": [ "refinePeaks" ] }, { "page": "refineSites", "title": "Adjust ChIP-seq Read Count Table", "topics": [ "refineSites" ] } ], "_readme": "https://github.com/bioc/gcapc/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "BSgenome", "cigarillo", "codetools", "cpp11", "crayon", "curl", "DelayedArray", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "httr", "IRanges", "jsonlite", "lambda.r", "lattice", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mime", "openssl", "R6", "RCurl", "restfulr", "Rhtslib", "rjson", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "gcapc.Rmd", "filename": "gcapc.html", "title": "The gcapc user's guide", "author": "| Mingxiang Teng mxteng@jimmy.harvard.edu | Rafael A. Irizarry rafa@jimmy.harvard.edu | Department of Biostatistics, Dana-Farber Cancer Institute & | Harvard T.H. Chan School of Public Health, Boston, MA, USA", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting Started", "Preparing Inputs", "Peak Calling/Refining", "Reads coverage", "Binding width", "GC effects", "Peak significance", "Peak refining", "Correcting GC Effects for A Count Table", "Summary", "References" ], "created": "2016-10-19 15:02:19", "modified": "2017-06-08 19:17:18", "commits": 19 } ], "_score": 5.380211241711606, "_indexed": false, "_nocasepkg": "gcapc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/gcapc", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.36.0", "date": "2026-06-11T07:11:25.000Z", "distro": "noble", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "c0db73320017f664c96d34e1de13116683bd1b1df39c26d280be12fde6081309", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.6.0", "os": "linux", "version": "1.36.0", "date": "2026-06-11T07:09:09.000Z", "distro": "noble", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "7510e9a27b50275e821a12facc019f7f8ef46382347c4c72c95b9663e00bfe1e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.5.3", "os": "mac", "version": "1.36.0", "date": "2026-06-11T07:10:04.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "977b36d0d04786eb89d54155e198cdd8f618cee76d0f92e2223e1e2c5790c655", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.6.0", "os": "mac", "version": "1.36.0", "date": "2026-06-11T07:09:01.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "0917aa00cfcc846d1c9ab177257579e94afcbf2fb64ef52d9fb9b42bc4441572", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.6.0", "os": "wasm", "version": "1.36.0", "date": "2026-06-11T07:08:14.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "ddecac9170556675a6e282edeebf031e5b37dc54ed12fbc5d742922135956a39", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.7.0", "os": "win", "version": "1.36.0", "date": "2026-06-11T07:06:42.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "7d0883f55d51e5a67a79d6105512b933bdc8ec4327026f9cfe4d670f139a0fa4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.5.3", "os": "win", "version": "1.36.0", "date": "2026-06-11T07:06:48.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "6e6715928f5b8fe4f948e6472687f888d17d441f984f0d7c31a69ca136b7488a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" }, { "r": "4.6.0", "os": "win", "version": "1.36.0", "date": "2026-06-11T07:07:00.000Z", "commit": "8512c5cf23413c0748182ff23a89a5c64d43e7d0", "fileid": "95d2f40c5107d40c169b0a8723ff14351aa364035d22b7ec3a7decc99c896afa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27329550803" } ] }