{ "_id": "6ac8fb54de46216d5edd9575", "Package": "csaw", "Version": "1.46.0", "Date": "2025-06-20", "Title": "ChIP-Seq Analysis with Windows", "Authors@R": "c(person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(\"Gordon\", \"Smyth\", role=\"aut\"))", "biocViews": "MultipleComparison, ChIPSeq, Normalization, Sequencing,\nCoverage, Genetics, Annotation, DifferentialPeakCalling", "Description": "Detection of differentially bound regions in ChIP-seq data\nwith sliding windows, with methods for normalization and proper\nFDR control.", "License": "GPL-3", "NeedsCompilation": "yes", "SystemRequirements": "C++11, GNU make", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:40:01 UTC", "RemoteUrl": "https://github.com/bioc/csaw", "RemoteRef": "RELEASE_3_23", "RemoteSha": "ce50500871243747fae230c752dc2d4fec5093ee", "Packaged": { "Date": "2026-10-09 14:11:43 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre],\nGordon Smyth [aut]", "Maintainer": "Aaron Lun ", "_user": "bioc-release", "_type": "src", "_file": "csaw_1.46.0.tar.gz", "_fileid": "https://r2.ropensci.org/e9e4d86e41bf34fb41aaea4ea8153e517bd54c402dd9d1208198885d49317abf", "_filesize": 531569, "_sha256": "e9e4d86e41bf34fb41aaea4ea8153e517bd54c402dd9d1208198885d49317abf", "_expires": "2027-01-17T14:33:54.000Z", "_created": "2026-10-09T14:11:43.000Z", "_published": "2026-10-09T14:33:56.158Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 2, "note": 9 }, "_upstream": "https://github.com/bioc/csaw", "_commit": { "id": "ce50500871243747fae230c752dc2d4fec5093ee", "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": 1777380001 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_distro": "resolute", "_jobs": [ { "job": 113860316599, "time": 265, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11622331189" }, { "job": 113860316723, "time": 471, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "11622166993" }, { "job": 113860316740, "time": 653, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11622337971" }, { "job": 113860316833, "time": 450, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11621942064" }, { "job": 113860316773, "time": 470, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11622397334" }, { "job": 113860316946, "time": 370, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11622242711" }, { "job": 113860316909, "time": 847, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11622354751" }, { "job": 113860316905, "time": 491, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11622343797" }, { "job": 113860316743, "time": 765, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11622509192" }, { "job": 113857595689, "time": 385, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11621769267" }, { "job": 113860316845, "time": 252, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11622926267" }, { "job": 113860317140, "time": 627, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11622787482" }, { "job": 113860316807, "time": 638, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11622607532" }, { "job": 113860316888, "time": 596, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11623047283" }, { "job": 113860316858, "time": 620, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11622297378" }, { "job": 113860316914, "time": 483, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11622996827" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "GenomicRanges", "version": ">= 1.61.1", "role": "Depends" }, { "package": "SummarizedExperiment", "version": ">= 1.39.1", "role": "Depends" }, { "package": "Rhtslib", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "metapod", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "AnnotationDbi", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "TxDb.Mmusculus.UCSC.mm10.knownGene", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "GenomicFeatures", "role": "Suggests" }, { "package": "GenomicAlignments", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 9, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.1", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "multiplecomparison", "chipseq", "normalization", "sequencing", "coverage", "genetics", "annotation", "differentialpeakcalling", "curl", "bzip2", "xz-utils", "zlib", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1282, "source": "https://www.bioconductor.org/packages/stats/bioc/csaw" }, "_mentions": 29, "_searchresults": 635, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/csaw.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "asDGEList", "calculateCPM", "checkBimodality", "clusterFDR", "clusterWindows", "clusterWindowsList", "combineOverlaps", "combineTests", "consolidateOverlaps", "consolidateTests", "consolidateWindows", "controlClusterFDR", "correlateReads", "csawUsersGuide", "detailRanges", "empiricalFDR", "empiricalOverlaps", "extractReads", "filterWindows", "filterWindowsControl", "filterWindowsGlobal", "filterWindowsLocal", "filterWindowsProportion", "findMaxima", "findOverlapsList", "getBestOverlaps", "getBestTest", "getPESizes", "getWidths", "maximizeCcf", "mergeResults", "mergeResultsList", "mergeWindows", "mergeWindowsList", "minimalTests", "mixedClusters", "mixedOverlaps", "mixedTests", "normFactors", "normOffsets", "overlapResults", "overlapResultsList", "profileSites", "readParam", "reform", "regionCounts", "scaleControlFilter", "scaledAverage", "show", "strandedCounts", "summitOverlaps", "upweightSummit", "windowCounts", "wwhm" ], "_help": [ { "page": "calculateCPM", "title": "Calculate CPM", "topics": [ "calculateCPM" ] }, { "page": "checkBimodality", "title": "Check bimodality of regions", "topics": [ "checkBimodality" ] }, { "page": "cluster-direction", "title": "Reporting cluster-level direction in 'csaw'", "topics": [ "cluster-direction" ] }, { "page": "clusterFDR", "title": "Compute the cluster-level FDR", "topics": [ "clusterFDR", "controlClusterFDR" ] }, { "page": "clusterWindows", "title": "Cluster DB windows into clusters", "topics": [ "clusterWindows" ] }, { "page": "clusterWindowsList", "title": "Consolidate DB clusters", "topics": [ "clusterWindowsList" ] }, { "page": "combineTests", "title": "Combine statistics across multiple tests", "topics": [ "combineTests" ] }, { "page": "correlateReads", "title": "Compute correlation coefficients between reads", "topics": [ "correlateReads" ] }, { "page": "csawUsersGuide", "title": "View csaw user's guide", "topics": [ "csaw", "csawUsersGuide" ] }, { "page": "defunct", "title": "Defunct functions", "topics": [ "consolidateOverlaps", "consolidateTests", "consolidateWindows", "defunct", "filterWindows" ] }, { "page": "detailRanges", "title": "Add annotation to ranges", "topics": [ "detailRanges" ] }, { "page": "empiricalFDR", "title": "Control the empirical FDR", "topics": [ "empiricalFDR" ] }, { "page": "extractReads", "title": "Extract reads from a BAM file", "topics": [ "extractReads" ] }, { "page": "filterWindows", "title": "Filtering methods for RangedSummarizedExperiment objects", "topics": [ "filterWindowsControl", "filterWindowsGlobal", "filterWindowsLocal", "filterWindowsProportion", "scaleControlFilter" ] }, { "page": "findMaxima", "title": "Find local maxima", "topics": [ "findMaxima" ] }, { "page": "getBestTest", "title": "Get the best test in a cluster", "topics": [ "getBestTest" ] }, { "page": "getPESizes", "title": "Compute fragment lengths for paired-end tags", "topics": [ "getPESizes" ] }, { "page": "getWidths", "title": "Get region widths", "topics": [ "getWidths" ] }, { "page": "maximizeCcf", "title": "Find the delay at the maximal CCF", "topics": [ "maximizeCcf" ] }, { "page": "mergeWindows", "title": "Merge windows into clusters", "topics": [ "mergeWindows" ] }, { "page": "mergeWindowsList", "title": "Consolidate window sizes", "topics": [ "findOverlapsList", "mergeWindowsList" ] }, { "page": "minimalTests", "title": "Require rejection of a minimal number of tests", "topics": [ "minimalTests" ] }, { "page": "mixedTests", "title": "Tests for mixed DB clusters", "topics": [ "mixedClusters", "mixedTests" ] }, { "page": "normFactors", "title": "Scaling normalization across libraries", "topics": [ "normFactors" ] }, { "page": "normOffsets", "title": "Normalize trended biases across libraries", "topics": [ "normOffsets" ] }, { "page": "overlapStats", "title": "Combine statistics for overlap-based clusters", "topics": [ "combineOverlaps", "empiricalOverlaps", "getBestOverlaps", "mixedOverlaps", "overlapStats", "summitOverlaps" ] }, { "page": "profileSites", "title": "Profile binding sites", "topics": [ "profileSites" ] }, { "page": "readParam", "title": "readParam class and methods", "topics": [ "$,readParam-method", "readParam", "readParam-class", "reform", "reform,readParam-method", "show,readParam-method" ] }, { "page": "regionCounts", "title": "Count reads overlapping each region", "topics": [ "regionCounts" ] }, { "page": "mergeResults", "title": "Wrappers to get region-level results", "topics": [ "mergeResults", "overlapResults" ] }, { "page": "mergeResultsList", "title": "Wrappers to combine multiple analyses", "topics": [ "mergeResultsList", "overlapResultsList" ] }, { "page": "scaledAverage", "title": "Scaled average abundance", "topics": [ "scaledAverage" ] }, { "page": "SEmethods", "title": "SummarizedExperiment to DGEList", "topics": [ "asDGEList", "asDGEList,SummarizedExperiment-method" ] }, { "page": "strandedCounts", "title": "Get strand-specific counts", "topics": [ "strandedCounts" ] }, { "page": "upweightSummit", "title": "Upweight summits", "topics": [ "upweightSummit" ] }, { "page": "windowCounts", "title": "Count reads overlapping each window", "topics": [ "windowCounts" ] }, { "page": "wwhm", "title": "Window width at half maximum", "topics": [ "wwhm" ] } ], "_readme": "https://github.com/bioc/csaw/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "codetools", "cpp11", "crayon", "DelayedArray", "edgeR", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "IRanges", "lambda.r", "lattice", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "metapod", "Rcpp", "Rhtslib", "Rsamtools", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "statmod", "SummarizedExperiment", "XVector" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.18.0-1ubuntu2.7", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libbz2", "package": "libbz2-1.0", "headers": "libbz2-dev", "source": "bzip2", "version": "1.0.8-6ubuntu0.1", "name": "bzip2", "homepage": "https://sourceware.org/bzip2/", "description": "high-quality block-sorting file compressor library - runtime" }, { "shlib": "liblzma", "package": "liblzma5", "headers": "liblzma-dev", "source": "xz-utils", "version": "5.8.3-1", "name": "xz-utils", "homepage": "https://tukaani.org/xz/", "description": "XZ-format compression library" }, { "shlib": "libz", "package": "zlib1g", "headers": "zlib1g-dev", "source": "zlib", "version": "1:1.3.dfsg+really1.3.1-1ubuntu3.1", "name": "zlib", "homepage": "http://zlib.net/", "description": "compression library - runtime" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "csaw.Rmd", "filename": "csaw.html", "title": "Introducing the csaw package", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Documentation", "Session information" ], "created": "2019-02-17 17:46:31", "modified": "2020-11-26 07:58:12", "commits": 5 } ], "_score": 8.342025514633761, "_indexed": false, "_nocasepkg": "csaw", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/csaw", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.46.0", "date": "2026-10-09T14:15:41.000Z", "distro": "resolute", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/7728275636d10dfb9de3563d168059ff1b85b7f2678acd10f0b549a1cd54745a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.7.0", "os": "linux", "version": "1.46.0", "date": "2026-10-09T14:19:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/6b09b428c723ee1745cea34c2cd4dd3ba4116feb56a61c810b3d080987801d6d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "linux", "version": "1.46.0", "date": "2026-10-09T14:15:35.000Z", "distro": "resolute", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/dbf6427e7e8bf307a9927ea6e2ee77e9bfa1ffe94ef92466bd036bfbf4d74905", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "linux", "version": "1.46.0", "date": "2026-10-09T14:16:58.000Z", "distro": "resolute", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/8fa13c01518d54000ad1e5a3a54ae6cdc3482e70b5796e7ac7337de5f563ba8f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.5.3", "os": "mac", "version": "1.46.0", "date": "2026-10-09T14:21:25.000Z", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/b0555ffb7e3b2668dd1bb0e35308cf1f012c927ea6eec3186531c1527734a474", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.5.3", "os": "mac", "version": "1.46.0", "date": "2026-10-09T14:23:04.000Z", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/7d70d27ae717274148433ab78b390725d0c3ef3e08442f0dfce08f94782ae294", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "mac", "version": "1.46.0", "date": "2026-10-09T14:22:16.000Z", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/50661a586cef0ef9d5319e44e8255642833c68151cb521e8a90b49de4ee7af82", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "mac", "version": "1.46.0", "date": "2026-10-09T14:23:31.000Z", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/faaa0661bba054e5964c5590ec90c516e056e1046e0bb813b77ded11f35059a4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.0", "os": "wasm", "version": "1.46.0", "date": "2026-10-09T14:15:55.000Z", "arch": "emscripten", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/bdef055cac7982ddb2bc77f59b6d46a9e1ba988c063dc52b19da6be8628c57b4", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.7.0", "os": "win", "version": "1.46.0", "date": "2026-10-09T14:17:15.000Z", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/1497b6349baec16d33c5768577daf8733fc4e3ffed301251c5b59b146d6bf122", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.7.0", "os": "win", "version": "1.46.0", "date": "2026-10-09T14:15:02.000Z", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/bf6eafea535a25fb09d5a36e853c05afe74af38f6c9e4f9f3b4c3e0b9b0e1467", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.5.3", "os": "win", "version": "1.46.0", "date": "2026-10-09T14:14:52.000Z", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/280e4e18301720c12a16bc2e7f06a12f594974aa6d2f3c7f30f89b24b758622f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "win", "version": "1.46.0", "date": "2026-10-09T14:17:19.000Z", "arch": "aarch64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/997a34e94c2bd67720f92b33e78b60ecc01e5f7c2df246c3c0f133b4139e875f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" }, { "r": "4.6.1", "os": "win", "version": "1.46.0", "date": "2026-10-09T14:15:42.000Z", "arch": "x86_64", "commit": "ce50500871243747fae230c752dc2d4fec5093ee", "fileid": "https://r2.ropensci.org/46d1a77e8ddf917dd7538a54f0ccda387dd4d0ba6a80361bb7bb9eb0d8ef3fae", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37941709892" } ] }