{ "_id": "6a12de29acfb0bcc41d230df", "Package": "quaqcr", "Title": "Quick ATAC-Seq QC", "Version": "1.0.4.9000", "Authors@R": "person(c(\"Benjamin\", \"Jean-Marie\"), \"Tremblay\", role = c(\"aut\", \"cre\"),\nemail = \"benjmtremblay@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7441-2951\"))", "Description": "A wrapper around the 'quaqc' program described in Tremblay\nand Questa (2024) . 'quaqc'\nallows for assay for transposase-accessible chromatin using\nsequencing (ATAC-seq) specific quality control and read\nfiltering of next-generation sequencing (NGS) data with minimal\nprocessing time and extremely low memory overhead. Any number\nof samples can be processed, using multiple threads if desired.\n'quaqc' outputs a comprehensive set of aligned read metrics,\nincluding alignment size, fragment size, percent duplicates,\nmapq scores, read depth, GC content, and others. Although\ndesigned for ATAC-seq data, 'quaqc' can also be used for other\nunspliced DNA sequencing experiments (such as chromatin\nimmunoprecipitation sequencing, or ChIP-seq) as many of the\nmetrics are related to general sequencing quality. This R\npackage also provides additional utilities for custom analyses\nand plotting of 'quaqc' results.", "URL": "https://github.com/bjmt/quaqcr", "BugReports": "https://github.com/bjmt/quaqcr/issues", "License": "GPL (>= 3)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE, old_usage = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "SystemRequirements": "quaqc (https://github.com/bjmt/quaqc)", "Repository": "https://bjmt.r-universe.dev", "Date/Publication": "2026-05-24 09:50:20 UTC", "RemoteUrl": "https://github.com/bjmt/quaqcr", "RemoteRef": "HEAD", "RemoteSha": "cb4a0ec40a7a378999bf97765c0358b38b65dc5c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-24 11:14:23 UTC", "User": "root" }, "Author": "Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:\n)", "Maintainer": "Benjamin Jean-Marie Tremblay ", "MD5sum": "7f7fd9ddfa3a8a88d9427da4f0218e76", "_user": "bjmt", "_type": "src", "_file": "quaqcr_1.0.4.9000.tar.gz", "_fileid": "2b991ec940e0af9356c85a46a41e9597fdd05d8cc7f0a7c0091ae802df07ecdb", "_filesize": 979833, "_sha256": "2b991ec940e0af9356c85a46a41e9597fdd05d8cc7f0a7c0091ae802df07ecdb", "_created": "2026-05-24T11:14:23.000Z", "_published": "2026-05-24T11:16:57.064Z", "_distro": "noble", "_jobs": [ { "job": 77592835226, "time": 124, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7184677950" }, { "job": 77592835245, "time": 118, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7184677213" }, { "job": 77592835230, "time": 78, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7184673285" }, { "job": 77592835234, "time": 84, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7184673707" }, { "job": 77592718682, "time": 129, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7184665280" }, { "job": 77592835228, "time": 106, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7184676007" }, { "job": 77592835231, "time": 66, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7184672121" }, { "job": 77592835236, "time": 65, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7184672013" }, { "job": 77592835229, "time": 65, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7184671903" } ], "_buildurl": "https://github.com/r-universe/bjmt/actions/runs/26359654640", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bjmt/quaqcr", "_commit": { "id": "cb4a0ec40a7a378999bf97765c0358b38b65dc5c", "author": "Benjamin Jean-Marie Tremblay ", "committer": "Benjamin Jean-Marie Tremblay ", "message": "add helpers to read quaqc output files\n\nread_bedgraph(), read_bed(), read_narrowpeak(), read_qscore(), and\nread_quant() take a quaqc/quaqc_report object and load the corresponding\noutput files. Paths are derived from each sample's BAM filename with\noptional dir/ext overrides matching the quaqc() arguments. The filtered\nBAM (--keep) output is intentionally excluded.\n", "time": 1779616220 }, "_maintainer": { "name": "Benjamin Jean-Marie Tremblay", "email": "benjmtremblay@gmail.com", "login": "bjmt", "orcid": "0000-0002-7441-2951", "description": "", "uuid": 24674853 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bjmt", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 5 }, { "week": "2026-21", "n": 5 } ], "_tags": [ { "name": "v1.0.1", "date": "2026-05-05" }, { "name": "v1.0.2", "date": "2026-05-07" }, { "name": "v1.0.3", "date": "2026-05-09" }, { "name": "v1.0.4", "date": "2026-05-22" } ], "_stars": 1, "_contributors": [ { "user": "bjmt", "count": 30, "uuid": 24674853 } ], "_userbio": { 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sections of a quaqc report into a data.frame.", "topics": [ "melt_reports" ] }, { "page": "parse_quaqc", "title": "Parse a JSON quaqc report file.", "topics": [ "parse_quaqc", "parse_quaqc_file" ] }, { "page": "pileup", "title": "Generate read pileups from BAMs with quaqc.", "topics": [ "pileup" ] }, { "page": "quaqc", "title": "Run quaqc from within R.", "topics": [ "quaqc" ] }, { "page": "quaqcr-pkg", "title": "quaqcr: Quick ATAC-seq QC in R", "topics": [ "quaqcr-package", "quaqcr", "quaqcr-pkg" ] }, { "page": "read_quaqc_output", "title": "Read quaqc output files associated with a report.", "topics": [ "read_bed", "read_bedgraph", "read_narrowpeak", "read_qscore", "read_quant", "read_quaqc_output" ] } ], "_readme": "https://github.com/bjmt/quaqcr/raw/HEAD/README.md", "_rundeps": [ "jsonlite" ], "_score": 3, "_indexed": true, "_nocasepkg": "quaqcr", "_universes": [ "bjmt" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4.9000", "date": "2026-05-24T11:16:28.000Z", 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