{ "_id": "6a14290facfb0bcc41d40492", "Package": "BiFET", "Type": "Package", "Title": "Bias-free Footprint Enrichment Test", "Version": "1.33.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:47:07 UTC", "RemoteUrl": "https://github.com/bioc/BiFET", "RemoteRef": "HEAD", "RemoteSha": "e6d1543055fc5419354db78e4e38049463b9c6ad", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 10:43:30 UTC", "User": "root" }, "Author": "Ahrim Youn [aut, cre],\nEladio Marquez [aut],\nNathan Lawlor [aut],\nMichael Stitzel [aut],\nDuygu Ucar [aut]", "MD5sum": "6dfb6316ba897f23ddae651f4a2e72a2", "_user": "bioc", "_type": "src", "_file": "BiFET_1.33.0.tar.gz", "_fileid": "8e65c55be46b10d0f178b1ff873d4911841842691c6f76c47bb7a490278a5a5b", "_filesize": 520643, "_sha256": "8e65c55be46b10d0f178b1ff873d4911841842691c6f76c47bb7a490278a5a5b", "_created": "2026-05-25T10:43:30.000Z", "_published": "2026-05-25T10:48:47.014Z", "_jobs": [ { "job": 77698154921, "time": 148, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7196670567" }, { "job": 77698154924, "time": 203, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7196683992" }, { "job": 77698154932, "time": 208, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7196685633" }, { "job": 77698154935, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7196662448" }, { "job": 77698154928, "time": 122, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7196664517" }, { "job": 77697731512, "time": 201, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7196633167" }, { "job": 77698154931, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7196660533" }, { "job": 77698154933, "time": 277, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7196702177" }, { "job": 77698154975, "time": 246, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7196695043" }, { "job": 77698154965, "time": 255, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7196696922" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BiFET", "_commit": { "id": "e6d1543055fc5419354db78e4e38049463b9c6ad", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following 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": true, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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/HEAD/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": true, "_nocasepkg": "bifet", "_universes": [ "bioc", "youna2" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-05-25T10:45:40.000Z", "distro": "noble", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "bb441610ba0aae48649e8366760f55a00074cce5c542e1305a216c6f20f2d2fc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.6.0", "os": "linux", "version": "1.33.0", "date": "2026-05-25T10:45:47.000Z", "distro": "noble", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "d4ff1ccc0b561d68f7a2c0c7718c5c6195ca3ee6d0fdbd82af1425018a62b141", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.5.3", "os": "mac", "version": "1.33.0", "date": "2026-05-25T10:44:57.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "9e6c8d136b366b0895443ce341d8981d677f01ec155a6eaa32226fdacb3cfd75", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.6.0", "os": "mac", "version": "1.33.0", "date": "2026-05-25T10:44:57.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "404d214297dd808ee1af7cb6a194b5bad7d2d9642e694b722195a30f03dc8e28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.6.0", "os": "wasm", "version": "1.33.0", "date": "2026-05-25T10:45:37.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "5b4a39272a69709377cecb16a1da6ab9a18e86fe74104daf6e78ab116b0ad577", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.7.0", "os": "win", "version": "1.33.0", "date": "2026-05-25T10:44:52.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "c450bcc006d9cae102222f2d7699afef986ce368b0a82afbf74f8036ec82382b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.5.3", "os": "win", "version": "1.33.0", "date": "2026-05-25T10:44:43.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "d5ea53bb02272cc975fdb019c65feb8e3c1fe36faf2b609bce50495717882733", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" }, { "r": "4.6.0", "os": "win", "version": "1.33.0", "date": "2026-05-25T10:44:46.000Z", "commit": "e6d1543055fc5419354db78e4e38049463b9c6ad", "fileid": "f0ce8432fb4c3b5064498eebe4f2e134c65531bde38cb40594e962f2a388a341", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26396309741" } ] }