{ "_id": "6a4973ecf408bf5a1e5fde7d", "Package": "metapod", "Version": "1.21.0", "Date": "2026-02-18", "Title": "Meta-Analyses on P-Values of Differential Analyses", "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"aut\", \"cre\"), email = \"infinite.monkeys.with.keyboards@gmail.com\")", "biocViews": "MultipleComparison, DifferentialPeakCalling", "Description": "Implements a variety of methods for combining p-values in\ndifferential analyses of genome-scale datasets. Functions can\ncombine p-values across different tests in the same analysis\n(e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for\ncorresponding tests across separate analyses (e.g., replicated\ncomparisons, effect of different treatment conditions). Support\nis provided for handling log-transformed input p-values,\nmissing values and weighting where appropriate.", "License": "GPL-3", "URL": "https://github.com/LTLA/metapod", "BugReports": "https://github.com/LTLA/metapod/issues", "NeedsCompilation": "yes", "SystemRequirements": "C++11", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:31 UTC", "RemoteUrl": "https://github.com/bioc/metapod", "RemoteRef": "HEAD", "RemoteSha": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "Packaged": { "Date": "2026-06-23 15:09:13 UTC", "User": "root" }, "Author": "Aaron Lun [aut, cre]", "Maintainer": "Aaron Lun ", "_user": "bioc", "_type": "src", "_file": "metapod_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/270fbd1382eed4d33aceee98a91f157d807903d1a3efc48335db7ee9e3e44b3d", "_filesize": 229095, "_sha256": "270fbd1382eed4d33aceee98a91f157d807903d1a3efc48335db7ee9e3e44b3d", "_expires": "2026-10-12T20:58:19.000Z", "_created": "2026-06-23T15:09:13.000Z", "_published": "2026-07-04T20:58:20.905Z", "_bioccheck": { "error": 0, "warning": 1, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097", "_status": "success", "_upstream": "https://github.com/bioc/metapod", "_commit": { "id": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380871 }, "_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": 85166449570, "time": 161, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7825012260" }, { "job": 85166449590, "time": 184, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7825024674" }, { "job": 85166449529, "time": 188, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7825024278" }, { "job": 85166449596, "time": 146, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7825007380" }, { "job": 85166449536, "time": 196, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7825026676" }, { "job": 85166449591, "time": 147, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7825005823" }, { "job": 85166449564, "time": 296, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7825068944" }, { "job": 85166449618, "time": 135, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7825000819" }, { "job": 85166449431, "time": 291, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7825067791" }, { "job": 85166449419, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7824941880" }, { "job": 85166449416, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7824995938" }, { "job": 85166449512, "time": 166, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7825014441" }, { "job": 85166449483, "time": 143, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7825004472" }, { "job": 85166449520, "time": 142, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7825004057" } ], "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 54, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-47", "n": 2 }, { "week": "2026-08", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "multiplecomparison", "differentialpeakcalling", "cpp" ], "_stars": 2, "_contributors": [ { "user": "ltla", "count": 58, "uuid": 8166669 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 6, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/ltla/metapod", "_searchresults": 20, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/metapod.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/ltla/metapod", "_realowner": "bioc", "_cranurl": false, "_exports": [ "averageGroupedStats", "averageParallelStats", "combineGroupedPValues", "combineParallelPValues", "countGroupedDirection", "countParallelDirection", "groupedBerger", "groupedFisher", "groupedHolmMin", "groupedPearson", "groupedSimes", "groupedStouffer", "groupedWilkinson", "parallelBerger", "parallelFisher", "parallelHolmMin", "parallelPearson", "parallelSimes", "parallelStouffer", "parallelWilkinson", "summarizeGroupedDirection", "summarizeParallelDirection" ], "_help": [ { "page": "metapod-package", "title": "metapod: Meta-Analyses on P-Values of Differential Analyses", "topics": [ "metapod-package", "metapod" ] }, { "page": "averageGroupedStats", "title": "Average grouped statistics", "topics": [ "averageGroupedStats" ] }, { "page": "averageParallelStats", "title": "Average parallel statistics", "topics": [ "averageParallelStats" ] }, { "page": "combineGroupedPValues", "title": "Combine grouped p-values", "topics": [ "combineGroupedPValues" ] }, { "page": "combineParallelPValues", "title": "Combine parallel p-values", "topics": [ "combineParallelPValues" ] }, { "page": "countGroupedDirection", "title": "Count directions of grouped tests", "topics": [ "countGroupedDirection" ] }, { "page": "countParallelDirection", "title": "Count directions of parallel tests", "topics": [ "countParallelDirection" ] }, { "page": "groupedBerger", "title": "Combine grouped p-values with Berger's IUT", "topics": [ "groupedBerger" ] }, { "page": "groupedFisher", "title": "Combine grouped p-values with Fisher's method", "topics": [ "groupedFisher" ] }, { "page": "groupedHolmMin", "title": "Combine grouped p-values with the minimum Holm approach", "topics": [ "groupedHolmMin" ] }, { "page": "groupedPearson", "title": "Combine grouped p-values with Pearson's method", "topics": [ "groupedPearson" ] }, { "page": "groupedSimes", "title": "Combine grouped p-values with Simes' method", "topics": [ "groupedSimes" ] }, { "page": "groupedStouffer", "title": "Combine grouped p-values with Stouffer's Z-score method", "topics": [ "groupedStouffer" ] }, { "page": "groupedWilkinson", "title": "Combine grouped p-values with Wilkinson's method", "topics": [ "groupedWilkinson" ] }, { "page": "parallelBerger", "title": "Combine parallel p-values with Berger's IUT", "topics": [ "parallelBerger" ] }, { "page": "parallelFisher", "title": "Combine parallel p-values with Fisher's method", "topics": [ "parallelFisher" ] }, { "page": "parallelHolmMin", "title": "Combine parallel p-values with the minimum Holm approach", "topics": [ "parallelHolmMin" ] }, { "page": "parallelPearson", "title": "Combine parallel p-values with Pearson's method", "topics": [ "parallelPearson" ] }, { "page": "parallelSimes", "title": "Combine parallel p-values with Simes' method", "topics": [ "parallelSimes" ] }, { "page": "parallelStouffer", "title": "Combine parallel p-values with Stouffer's Z-score", "topics": [ "parallelStouffer" ] }, { "page": "parallelWilkinson", "title": "Combine p-values with Wilkinson's method", "topics": [ "parallelWilkinson" ] }, { "page": "summarizeGroupedDirection", "title": "Summarize overall direction of grouped tests", "topics": [ "summarizeGroupedDirection" ] }, { "page": "summarizeParallelDirection", "title": "Summarize overall direction of parallel tests", "topics": [ "summarizeParallelDirection" ] } ], "_readme": "https://github.com/bioc/metapod/raw/HEAD/README.md", "_rundeps": [ "Rcpp" ], "_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": "overview.Rmd", "filename": "overview.html", "title": "Meta-analyses on p-values of various differential tests", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Meta-analyses on $p$-values", "$p$-value combining strategies", "Summarizing the direction", "Further comments", "Session information" ], "created": "2020-11-02 06:27:32", "modified": "2021-05-12 07:09:49", "commits": 2 } ], "_score": 7.413634997198556, "_indexed": true, "_nocasepkg": "metapod", "_universes": [ "bioc", "ltla" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-23T15:12:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/f165dc89364118fe005e7adb886329ceaef22346a366357d76bf2b5024b4fb8c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-06-23T15:12:21.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/e7c545ddc4e41b5a6e57d61980b928ff73082b32774caff19172cd259ad0952f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-23T15:11:48.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/a3e4ec4274774a522edd643c522e9a33b4262540e301189a5bbc7fbd01b4f067", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-06-23T15:12:23.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/3c4f12793711bb0bcdff46cd20149ebdf8f0b5d2f6dcff47556e3f4b42c0a6ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-23T15:11:30.000Z", "arch": "aarch64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/7c0364d085601eaae7129a6c75d10c232553f31d386084e4c35cf65497ec70c6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-06-23T15:13:10.000Z", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/3bd73f3236c60395608727725831434ea8d7942158af48a3502d013734c613ef", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-23T15:11:14.000Z", "arch": "aarch64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/1d0ccca7bdd7c5324d88c3fdb6f7017596749ec64361394a85e724d1724dfbf8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-06-23T15:13:08.000Z", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/598caea809de350e547bf7bf2c2a822cc5cd516d954c844193763ab555ad0410", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-06-23T15:11:33.000Z", "arch": "emscripten", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/134e45ac1464eb4d9c2efccfd3f0055190ea9f2a93bf6779a2c1b19501c7b9eb", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-06-23T15:10:49.000Z", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/26c791aa9aa809085e0c59cadf884fc378002945301959af372f409367cfd558", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-06-23T15:10:56.000Z", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/c28e24fe2b238ac927268af558204c96a79e4d6a569748badb9e44728cfb6cad", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-06-23T15:10:44.000Z", "arch": "x86_64", "commit": "b1a66ff48329c4e0e6df918ca4bd9f0fa40755af", "fileid": "https://r2.ropensci.org/a4ea035bbf9ef5aec1b559af5432b82a4e707edf9d3c19f2f3d9c5a6adeb8030", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28035653097" } ] }