{ "_id": "6ad7238a4b18b900899991fd", "Package": "garfield", "Type": "Package", "Title": "GWAS Analysis of Regulatory or Functional Information Enrichment\nwith LD correction", "Version": "1.41.0", "Date": "2015-12-14", "Author": "Sandro Morganella ", "Maintainer": "Valentina Iotchkova ", "Description": "GARFIELD is a non-parametric functional enrichment\nanalysis approach described in the paper GARFIELD: GWAS\nanalysis of regulatory or functional information enrichment\nwith LD correction. Briefly, it is a method that leverages GWAS\nfindings with regulatory or functional annotations (primarily\nfrom ENCODE and Roadmap epigenomics data) to find features\nrelevant to a phenotype of interest. It performs greedy pruning\nof GWAS SNPs (LD r2 > 0.1) and then annotates them based on\nfunctional information overlap. Next, it quantifies Fold\nEnrichment (FE) at various GWAS significance cutoffs and\nassesses them by permutation testing, while matching for minor\nallele frequency, distance to nearest transcription start site\nand number of LD proxies (r2 > 0.8).", "biocViews": "Software, StatisticalMethod, Annotation,\nFunctionalPrediction, GenomeAnnotation", "License": "GPL-3", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:42:44 UTC", "RemoteUrl": "https://github.com/bioc/garfield", "RemoteRef": "HEAD", "RemoteSha": "81f058806f990f49cf9666d6336ca660990c9aa1", "Packaged": { "Date": "2026-10-20 08:11:10 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "garfield_1.41.0.tar.gz", "_fileid": "https://r2.ropensci.org/89a78a510ddb44674be1f0dd070c41f6a3b8bdfcb1ea312fab761013ed5a2b59", "_filesize": 434651, "_sha256": "89a78a510ddb44674be1f0dd070c41f6a3b8bdfcb1ea312fab761013ed5a2b59", "_expires": "2027-01-28T08:17:12.000Z", "_created": "2026-10-20T08:11:10.000Z", "_published": "2026-10-20T08:17:14.208Z", "_upstream": "https://github.com/bioc/garfield", "_status": "success", "_maintainer": { "name": "Valentina Iotchkova", "email": "vi1@sanger.ac.uk" }, "_jobs": [ { "job": 118524261267, "time": 117, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12250386055" }, { "job": 118524261297, "time": 143, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "12249942047" }, { "job": 118524261318, "time": 166, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12249558759" }, { "job": 118524261387, "time": 90, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12250161382" }, { "job": 118524261214, "time": 184, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12250156636" }, { "job": 118524261295, "time": 88, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "12250310562" }, { "job": 118524261257, "time": 291, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12249702827" }, { "job": 118524261219, "time": 92, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12249866927" }, { "job": 118524261233, "time": 165, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12250046968" }, { "job": 118523294187, "time": 147, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12250210969" }, { "job": 118524261136, "time": 90, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12249268589" }, { "job": 118524261346, "time": 194, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "12249872317" }, { "job": 118524261400, "time": 101, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "12249852136" }, { "job": 118524261383, "time": 68, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "12250116410" }, { "job": 118524261250, "time": 186, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "12249433975" }, { "job": 118524261396, "time": 87, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "12249986816" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118", "_commit": { "id": "81f058806f990f49cf9666d6336ca660990c9aa1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380164 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.41.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.40.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "statisticalmethod", "annotation", "functionalprediction", "genomeannotation", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 436, "source": "https://www.bioconductor.org/packages/stats/bioc/garfield" }, "_searchresults": 8, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/garfield.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "garfield_perm", "garfield_prep", "garfield.plot", "garfield.plot.fnx", "garfield.run" ], "_help": [ { "page": "garfield-package", "title": "GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction", "topics": [ "garfield-package", "garfield" ] }, { "page": "garfield.plot", "title": "Garfield plotting function", "topics": [ "garfield.plot" ] }, { "page": "garfield.plot.fnx", "title": "Internal radial plotting function for the garfield.plot function", "topics": [ "garfield.plot.fnx" ] }, { "page": "garfield.run", "title": "GARFIELD enrichment analysis function", "topics": [ "garfield.run", "garfield_perm", "garfield_prep" ] } ], "_rundeps": [], "_sysdeps": [ { "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": "vignette.Rnw", "filename": "vignette.pdf", "title": "garfield Guide", "engine": "knitr::knitr", "headings": [ "Introduction", "Installation" ], "created": "2016-02-25 23:50:48", "modified": "2018-08-30 17:49:02", "commits": 2 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "garfield", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-10-20T08:13:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/1c654313069583039573c89c3f530cf4dcb84e3616006c4ed678ad55f4db64ce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.7.0", "os": "linux", "version": "1.41.0", "date": "2026-10-20T08:13:56.000Z", "distro": "resolute", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/c82a2c2aec52b4504647096b1a61cfb4a09261494ad5f778f1347a766382dee9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "linux", "version": "1.41.0", "date": "2026-10-20T08:12:49.000Z", "distro": "resolute", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/b332d37a15f90e09d754e6d2f13e4120d0e50bcb2eb6205fed97fd80ed4d4cd5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "linux", "version": "1.41.0", "date": "2026-10-20T08:14:19.000Z", "distro": "resolute", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/53f2d9108d8de3aa2e453364bd78766c3f0b486873f2c3bdc4427b63348ccb7e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-10-20T08:13:17.000Z", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/9c63a294b4495d1b893910e16cfdb5bbb502a9f5603f94244eccbdab41a2bdbd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.5.3", "os": "mac", "version": "1.41.0", "date": "2026-10-20T08:15:41.000Z", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/423b3ab34edccda4b1a869c92c7031e10c2132c5514a9087baaad1457dfc62bc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "mac", "version": "1.41.0", "date": "2026-10-20T08:12:45.000Z", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/e69e376d8d51c5176fb012d868c922b272af3377e6207e3e57203dfb3083f363", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "mac", "version": "1.41.0", "date": "2026-10-20T08:13:50.000Z", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/8926cd49715a0340919ba5818793f39cf60ed9134ebb7c107750fbde405fac5b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.0", "os": "wasm", "version": "1.41.0", "date": "2026-10-20T08:12:54.000Z", "arch": "emscripten", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/28dfeffcb648c77454ee24bd56cf3e8c26a27107a0a9b4134905e7f036bee3c9", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-10-20T08:14:11.000Z", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/9134aef7b79eac6425c0b43be891f7999dc99fe220991220197b591f2b70dff0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.7.0", "os": "win", "version": "1.41.0", "date": "2026-10-20T08:12:08.000Z", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/b79420fd0147a05c5c3bf1a37469c3ae9d97b73f9dbac9a6a9b0488254268244", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.5.3", "os": "win", "version": "1.41.0", "date": "2026-10-20T08:12:08.000Z", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/bd8a0c392097e9cdc61380c60d4da37b29f92fd294ee4bb88d11ff7180a02c83", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "win", "version": "1.41.0", "date": "2026-10-20T08:14:03.000Z", "arch": "aarch64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/b372276e3fc689844f672dd1218a2fd0196aeab61b3f836c6ee82cc3a26fe57f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" }, { "r": "4.6.1", "os": "win", "version": "1.41.0", "date": "2026-10-20T08:12:15.000Z", "arch": "x86_64", "commit": "81f058806f990f49cf9666d6336ca660990c9aa1", "fileid": "https://r2.ropensci.org/55b8d0b843c2996283da005787f45a9e4a16c40c6c5784ce5e3e95d5a0c33bf8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39391291118" } ] }