{ "_id": "6a1e94661d7bb097a0a6b2f5", "Package": "apeglm", "Title": "Approximate posterior estimation for GLM coefficients", "Version": "1.34.0", "Authors@R": "c(\nperson(\"Anqi\", \"Zhu\", email = \"anqizhu@live.unc.edu\", role = c(\"aut\",\"cre\")),\nperson(\"Joshua\", \"Zitovsky\", role = \"ctb\"),\nperson(\"Joseph\", \"Ibrahim\", role = \"aut\"),\nperson(\"Michael\", \"Love\", role = \"aut\"))", "Maintainer": "Anqi Zhu ", "Description": "apeglm provides Bayesian shrinkage estimators for effect\nsizes for a variety of GLM models, using approximation of the\nposterior for individual coefficients.", "VignetteBuilder": "knitr, rmarkdown", "License": "GPL-2", "Encoding": "UTF-8", "biocViews": "ImmunoOncology, Sequencing, RNASeq, DifferentialExpression,\nGeneExpression, Bayesian", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:46:21 UTC", "RemoteUrl": "https://github.com/bioc/apeglm", "RemoteRef": "RELEASE_3_23", "RemoteSha": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-02 08:16:19 UTC", "User": "root" }, "Author": "Anqi Zhu [aut, cre],\nJoshua Zitovsky [ctb],\nJoseph Ibrahim [aut],\nMichael Love [aut]", "MD5sum": "644dcc91c003b5eef016881e3ff06aea", "_user": "bioc-release", "_type": "src", "_file": "apeglm_1.34.0.tar.gz", "_fileid": "880334491cf5ca88234ba02011a232d29496733e9dffa52273cb92b9a504fa07", "_filesize": 1106221, "_sha256": "880334491cf5ca88234ba02011a232d29496733e9dffa52273cb92b9a504fa07", "_created": "2026-06-02T08:16:19.000Z", "_published": "2026-06-02T08:29:26.497Z", "_jobs": [ { "job": 79028451072, "time": 210, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7352543259" }, { "job": 79028451210, "time": 299, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7352575192" }, { "job": 79028451164, "time": 371, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7352597446" }, { "job": 79028451191, "time": 353, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7352593017" }, { "job": 79028451362, "time": 365, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7352595690" }, { "job": 79028451161, "time": 232, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7352550744" }, { "job": 79028451120, "time": 381, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7352600792" }, { "job": 79028451131, "time": 241, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7352554013" }, { "job": 79028451272, "time": 707, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7352709956" }, { "job": 79027416419, "time": 382, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7352471364" }, { "job": 79028451250, "time": 179, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7352532295" }, { "job": 79028451122, "time": 320, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7352580605" }, { "job": 79028451129, "time": 284, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7352568936" }, { "job": 79028451229, "time": 308, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7352577428" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/apeglm", "_commit": { "id": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "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": 1777380381 }, "_maintainer": { "name": "Anqi Zhu", "email": "anqizhu@live.unc.edu", "login": "azhu513", "description": "Statistician @Genentech. Former Computational Biologist @23andMe. PhD of Biostatistics from the University of North Carolina Chapel Hill.", "uuid": 30045495 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "RcppNumerical", "role": "LinkingTo" }, { "package": "emdbook", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "airway", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 9, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "sequencing", "rnaseq", "differentialexpression", "geneexpression", "bayesian", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 7144, "source": "https://www.bioconductor.org/packages/stats/bioc/apeglm" }, "_mentions": 41, "_searchresults": 1312, "_rbuild": "4.6.0", "_assets": [ "extra/apeglm.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "apeglm", "bbEstDisp", "logLikNB", "svalue" ], "_help": [ { "page": "apeglm", "title": "Approximate posterior estimation for GLM coefficients", "topics": [ "apeglm" ] }, { "page": "bbEstDisp", "title": "Simple line-search estimator for dispersion of a beta binomial", "topics": [ "bbEstDisp" ] }, { "page": "logLikNB", "title": "Log likelihood for Negative Binomial", "topics": [ "logLikNB" ] }, { "page": "svalue", "title": "Local FSR to svalue", "topics": [ "svalue" ] } ], "_rundeps": [ "abind", "bbmle", "bdsmatrix", "Biobase", "BiocGenerics", "coda", "DelayedArray", "emdbook", "generics", "GenomicRanges", "IRanges", "lattice", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mvtnorm", "numDeriv", "plyr", "Rcpp", "RcppEigen", "RcppNumerical", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "apeglm.Rmd", "filename": "apeglm.html", "title": "Effect size estimation with apeglm", "author": "Anqi Zhu, Joseph G. Ibrahim, and Michael I. Love", "engine": "knitr::rmarkdown", "headings": [ "Typical RNA-seq call from DESeq2", "Acknowledgments", "Example RNA-seq analysis", "Running apeglm", "Specific coefficients", "Modeling zero-inflated counts", "Modeling ratios of counts", "Session Info", "References" ], "created": "2017-08-07 13:41:22", "modified": "2021-05-11 07:10:05", "commits": 30 } ], "_score": 8.7042690407431, "_indexed": false, "_nocasepkg": "apeglm", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/apeglm", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.34.0", "date": "2026-06-02T08:20:13.000Z", "distro": "noble", "arch": "aarch64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "75b4f6546434f8dfddb19c64357cddf08d372fe8475063bd06cb93796e502035", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.7.0", "os": "linux", "version": "1.34.0", "date": "2026-06-02T08:20:55.000Z", "distro": "noble", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "f0809063e2520a312ad5676fe046926a4b697bf0e1001c84a3bff0c9026b68f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "linux", "version": "1.34.0", "date": "2026-06-02T08:20:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "986cc4fd91c0e4756287d7b82227f8b851e24c626eff421edb3be99b2a190c93", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "linux", "version": "1.34.0", "date": "2026-06-02T08:20:43.000Z", "distro": "noble", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "baf188cbcfcffae48113fc28accf586f17bc205876b04715a246ad52992bab84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.5.3", "os": "mac", "version": "1.34.0", "date": "2026-06-02T08:18:57.000Z", "arch": "aarch64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "7e09d6c8c4ae1914074af575e4051ed78c56a5419edd2816c03c9bbb34ecb3bb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.5.3", "os": "mac", "version": "1.34.0", "date": "2026-06-02T08:20:26.000Z", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "4047757e2ae5ed7e457c9182142051aa5684a6f63a79acde7b628c44daf6155d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "mac", "version": "1.34.0", "date": "2026-06-02T08:19:14.000Z", "arch": "aarch64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "715e633127ceaa9c2073dff724381c6fb0a8bc03b8e641887b6873ded72b0785", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "mac", "version": "1.34.0", "date": "2026-06-02T08:23:42.000Z", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "3bb6cb674bb48f203c7d68f33e057aec557afef1b6853d9dd0300603703cec7f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "wasm", "version": "1.34.0", "date": "2026-06-02T08:20:01.000Z", "arch": "emscripten", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "f871c74c7fd61809839c8740fc0f99fb9bcf325f925289c581aad0ef33ba6f3d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.7.0", "os": "win", "version": "1.34.0", "date": "2026-06-02T08:19:41.000Z", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "93d23537cfe43bae870080c7df8bd52b585ab6e653e579e6cfbc4e81b88c4257", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.5.3", "os": "win", "version": "1.34.0", "date": "2026-06-02T08:18:54.000Z", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "27387a40c6460c3c4b41da5308cf5b1462a8e3809555c0dc7bfa5b00f583bc5f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" }, { "r": "4.6.0", "os": "win", "version": "1.34.0", "date": "2026-06-02T08:19:09.000Z", "arch": "x86_64", "commit": "685e82d2c5cdf91d3f0d04a4b96e4d4d61524b87", "fileid": "3795f48ed226015084112d45f4d760358439b0a1116a5a06b6cd08273a8959d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26807121254" } ] }