{ "_id": "6abe825699f7aa8c6aa56fda", "Package": "chipseqDB", "Title": "A Bioconductor Workflow to Detect Differential Binding in\nChIP-seq Data", "Version": "1.37.0", "Date": "2020-11-25", "Authors@R": "c(person(role=c(\"aut\",\"cre\"), \"Aaron\", \"Lun\", email = \"infinite.monkeys.with.keyboards@gmail.com\"),\nperson(role=\"aut\", \"Gordon \", \"Smyth\"))", "Description": "Describes a computational workflow for performing a DB\nanalysis with sliding windows. The aim is to facilitate the\npractical implementation of window-based DB analyses by\nproviding detailed code and expected output. The workflow\ndescribed here applies to any ChIP-seq experiment with multiple\nexperimental conditions and multiple biological samples in one\nor more of the conditions. It detects and summarizes DB regions\nbetween conditions in a de novo manner, i.e., without making\nany prior assumptions about the location or width of bound\nregions. Detected regions are then annotated according to their\nproximity to genes.", "License": "Artistic-2.0", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncologyWorkflow, Workflow, EpigeneticsWorkflow", "Workflow": "true", "NeedsCompilation": "no", "URL": "https://www.bioconductor.org/help/workflows/chipseqDB/", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:22 UTC", "RemoteUrl": "https://github.com/bioc/chipseqDB", "RemoteRef": "HEAD", "RemoteSha": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "Packaged": { "Date": "2026-10-01 15:37:04 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre],\nGordon Smyth [aut]", "Maintainer": "Aaron Lun ", "_user": "bioc", "_type": "src", "_file": "chipseqDB_1.37.0.tar.gz", "_fileid": "https://r2.ropensci.org/53ffc048f3bd1d2b0249b3446fadf9d130c73f675482e49e917351b2b23fc358", "_filesize": 58804, "_sha256": "53ffc048f3bd1d2b0249b3446fadf9d130c73f675482e49e917351b2b23fc358", "_expires": "2027-01-09T15:55:00.000Z", "_created": "2026-10-01T15:37:04.000Z", "_published": "2026-10-07T14:17:31.434Z", "_bioccheck": { "error": 0, "warning": 2, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118", "_status": "success", "_upstream": "https://github.com/bioc/chipseqDB", "_commit": { "id": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380022 }, "_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": 110448322174, "time": 222, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "11174367080" }, { "job": 110448322196, "time": 326, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11175092086" }, { "job": 110448322179, "time": 304, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11173654083" }, { "job": 110448322131, "time": 133, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11174464508" }, { "job": 110448322492, "time": 125, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11175586100" }, { "job": 110445637913, "time": 354, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11173583366" }, { "job": 110448322214, "time": 197, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11174327321" }, { "job": 110448322098, "time": 183, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11174986939" }, { "job": 110448322342, "time": 158, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11173908662" }, { "job": 110448322424, "time": 207, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11174587359" } ], "_registered": true, "_dependencies": [ { "package": "chipseqDBData", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "ChIPpeakAnno", "role": "Suggests" }, { "package": "Gviz", "role": "Suggests" }, { "package": "Rsamtools", "role": "Suggests" }, { "package": "TxDb.Mmusculus.UCSC.mm10.knownGene", "role": "Suggests" }, { "package": "csaw", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "rtracklayer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_topics": [ "immunooncologyworkflow", "workflow", "epigeneticsworkflow" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 471, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_rbuild": "4.6.1", "_assets": [ "extra/chipseqDB.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf" ], "_cranurl": false, "_exports": [], "_help": [], "_rundeps": [], "_vignettes": [ { "source": "intro.Rmd", "filename": "intro.html", "title": "Using Bioconductor to detect differential binding in ChIP-seq data", "author": "Aaron T. L. Lun, Gordon K. Smyth", "engine": "knitr::rmarkdown", "headings": [ "Redirection notice" ], "created": "2018-12-23 06:14:14", "modified": "2020-11-26 07:50:53", "commits": 3 }, { "source": "h3k9ac.Rmd", "filename": "h3k9ac.html", "title": "Detecting differential enrichment of H3K9ac in murine B cells", "author": "Aaron T. L. Lun, Gordon K. Smyth", "engine": "knitr::rmarkdown", "headings": [ "Redirection notice" ], "created": "2018-12-23 06:14:14", "modified": "2020-11-26 07:50:53", "commits": 14 }, { "source": "cbp.Rmd", "filename": "cbp.html", "title": "Detecting differential binding of CBP in mouse fibroblasts", "author": "Aaron T. L. Lun, Gordon K. Smyth", "engine": "knitr::rmarkdown", "headings": [ "Redirection notice" ], "created": "2018-12-23 06:14:14", "modified": "2020-11-26 07:50:53", "commits": 14 }, { "source": "h3k27me3.Rmd", "filename": "h3k27me3.html", "title": "Detecting differential enrichment of H3K27me3 in the mouse lung epithelium", "author": "Aaron T. L. Lun, Aliaksei Holik", "engine": "knitr::rmarkdown", "headings": [ "Redirection notice" ], "created": "2019-05-27 19:32:09", "modified": "2020-11-26 07:50:53", "commits": 13 } ], "_score": 2.9030899869919438, "_indexed": true, "_nocasepkg": "chipseqdb", "_universes": [ "bioc", "ltla" ], "_progress_url": "https://github.com/r-universe/bioc/actions/runs/37635408052", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-10-01T15:42:39.000Z", "distro": "resolute", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/0879bc6c56468367ae2081c824cb0608603bfad44edea58906a8c29e66c81584", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.6.1", "os": "linux", "version": "1.37.0", "date": "2026-10-01T15:42:23.000Z", "distro": "resolute", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/5edf581e1983741b8dae7e211f1d062b78b972ced3401c87790dfa0d1a7745f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-10-01T15:54:30.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/fdfa76b38696a3dede17c3f495bba10d9619274adc9ee9a0d313f67680a406cb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.6.1", "os": "mac", "version": "1.37.0", "date": "2026-10-01T15:54:22.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/a5633fcdd5d2de96f23430efbd96072848182ef1eba75eb6c0a687c3ec473ffd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-10-01T15:40:40.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/11ef141876622c7ab1750d9e7136f1fbdc37f4afd6a3cdf17fb9f4ff1ad529e6", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-10-01T15:40:16.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/c7aeeefe743c280b5efb1e163e188955b5f94bbd2bfe6cdbd4dd5b01cc29529d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-10-01T15:39:56.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/4f346762087c4e7b84e6a7a8d121ce343d5e90b97d2053278ad734bd02d8d6a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" }, { "r": "4.6.1", "os": "win", "version": "1.37.0", "date": "2026-10-01T15:40:42.000Z", "commit": "4316cbe7ae02efcb24daeaf9663f6378e0cffe51", "fileid": "https://r2.ropensci.org/0c2ab0651ec8d26800bc91f2c19c040bccc908b0f0c08cf246cafbc43d0058a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36884869118" } ] }