{ "_id": "6a196833acfb0bcc41de8531", "Package": "BiFET", "Type": "Package", "Title": "Bias-free Footprint Enrichment Test", "Version": "1.32.0", "Date": "2025-06-27", "Authors@R": "c(person(\"Ahrim\", \"Youn\", email = \"Ahrim.Youn@jax.org\",\nrole = c(\"aut\", \"cre\")), person(\"Eladio\", \"Marquez\",\nemail = \"Eladio.Marquez@jax.org\", role = c(\"aut\")),\nperson(\"Nathan\", \"Lawlor\", email = \"nathan.lawlor03@gmail.com\",\nrole = c(\"aut\")), person(\"Michael\", \"Stitzel\",\nemail = \"Michael.Stitzel@jax.org\", role = c(\"aut\")),person(\"Duygu\",\n\"Ucar\", email = \"Duygu.Ucar@jax.org\", role = c(\"aut\")))", "Maintainer": "Ahrim Youn ", "Description": "BiFET identifies TFs whose footprints are over-represented\nin target regions compared to background regions after\ncorrecting for the bias arising from the imbalance in read\ncounts and GC contents between the target and background\nregions. For a given TF k, BiFET tests the null hypothesis that\nthe target regions have the same probability of having\nfootprints for the TF k as the background regions while\ncorrecting for the read count and GC content bias. For this, we\nuse the number of target regions with footprints for TF k, t_k\nas a test statistic and calculate the p-value as the\nprobability of observing t_k or more target regions with\nfootprints under the null hypothesis.", "License": "GPL-3", "biocViews": "ImmunoOncology, Genetics, Epigenetics, Transcription,\nGeneRegulation, ATACSeq, DNaseSeq, RIPSeq, Software", "Encoding": "UTF-8", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:47:07 UTC", "RemoteUrl": "https://github.com/bioc/BiFET", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 08:16:23 UTC", "User": "root" }, "Author": "Ahrim Youn [aut, cre],\nEladio Marquez [aut],\nNathan Lawlor [aut],\nMichael Stitzel [aut],\nDuygu Ucar [aut]", "MD5sum": "286f7d70f37c5aed9f828c6bc759dbd4", "_user": "bioc-release", "_type": "src", "_file": "BiFET_1.32.0.tar.gz", "_fileid": "8926cc79bc69bf5087fc6b6bd34cf7a2255eed75e7860d11e7dd7d987e522e6c", "_filesize": 521143, "_sha256": "8926cc79bc69bf5087fc6b6bd34cf7a2255eed75e7860d11e7dd7d987e522e6c", "_created": "2026-05-29T08:16:23.000Z", "_published": "2026-05-29T10:19:31.331Z", "_jobs": [ { "job": 78463863177, "time": 147, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7286255959" }, { "job": 78463863211, "time": 263, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286289952" }, { "job": 78463863340, "time": 278, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286294110" }, { "job": 78463863281, "time": 128, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7288397763" }, { "job": 78463863302, "time": 181, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7288410889" }, { "job": 78463398991, "time": 196, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7286212523" }, { "job": 78463863142, "time": 121, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7286248487" }, { "job": 78463863187, "time": 284, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7286295806" }, { "job": 78463863367, "time": 278, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7286294617" }, { "job": 78463863376, "time": 298, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7286299830" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BiFET", "_commit": { "id": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "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": 1777380427 }, "_maintainer": { "name": "Ahrim Youn", "email": "ahrim.youn@jax.org", "login": "youna2", "description": "", "uuid": 35052840 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "poibin", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "genetics", "epigenetics", "transcription", "generegulation", "atacseq", "dnaseseq", "ripseq", "software" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 431, "source": "https://www.bioconductor.org/packages/stats/bioc/BiFET" }, "_searchresults": 4, "_rbuild": "4.6.0", "_assets": [ "extra/BiFET.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calculate_enrich_p" ], "_help": [ { "page": "calculate_enrich_p", "title": "Function to calculate p-value testing if footprints of a TF are over-represented in the target set of peaks compared to the background set of peaks correcting for the bias arising from the imbalance of GC-content and read counts between target and background set", "topics": [ "calculate_enrich_p" ] } ], "_readme": "https://github.com/bioc/BiFET/raw/RELEASE_3_23/README.md", "_rundeps": [ "BiocGenerics", "generics", "GenomicRanges", "IRanges", "poibin", "S4Vectors", "Seqinfo" ], "_vignettes": [ { "source": "BiFET.Rmd", "filename": "BiFET.html", "title": "A Guide to using BiFET", "author": "Ahrim Youn", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "1. Obtaining a Peak File", "2. Obtaining a Matrix of Footprint Calls", "3. Calculating enrichment p-value", "Citing BiFET", "References" ], "created": "2017-12-20 16:28:32", "modified": "2018-05-17 19:51:21", "commits": 11 } ], "_score": 4.176091259055681, "_indexed": false, "_nocasepkg": "bifet", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/BiFET", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T08:19:28.000Z", "distro": "noble", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "fa542582e64a997dd400b4e58a12d63d5bd072ba20e7c4901eb9e68accbefe09", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.6.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T08:19:47.000Z", "distro": "noble", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "45d048bf95c401d1330af4f96161f049786be1f1205777645f41443202a21298", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.5.3", "os": "mac", "version": "1.32.0", "date": "2026-05-29T10:17:33.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "ff839391d99075cac06e04bcd40581fafbfbf7f13125247ff44219e53228caf6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.6.0", "os": "mac", "version": "1.32.0", "date": "2026-05-29T10:17:55.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "dcf2c20e72d6577b31dbe18f665e55812dd89f2769b967f0be5fce39c9508b04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.6.0", "os": "wasm", "version": "1.32.0", "date": "2026-05-29T08:18:41.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "178677ef1c0d6ba590dbd5a2d600fdca8d95cc34064d47e8466e172f6d4af54c", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.7.0", "os": "win", "version": "1.32.0", "date": "2026-05-29T08:17:51.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "266f0109a9a00c3fe603840156728b8f2134b4017ed57e6a20b80d57f77fe4c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.5.3", "os": "win", "version": "1.32.0", "date": "2026-05-29T08:17:47.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "09da2894566eee5e3f0d801d57626f1ede2fd82822b036db3ffe0a8fa49dce4b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" }, { "r": "4.6.0", "os": "win", "version": "1.32.0", "date": "2026-05-29T08:17:45.000Z", "commit": "0d5bbce2804e9ee7821d865d2b7502e765f29a6e", "fileid": "3bdcffd376871a0b22822548f7e22906caa6edf765f7b7e109fbc80cc48e6f01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26626171095" } ] }