{ "_id": "6a169e1cacfb0bcc41d7f544", "Package": "glmGamPoi", "Type": "Package", "Title": "Fit a Gamma-Poisson Generalized Linear Model", "Version": "1.25.1", "Authors@R": "c(person(\"Constantin\", \"Ahlmann-Eltze\", email = \"artjom31415@googlemail.com\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3762-068X\")),\nperson(\"Nathan\", \"Lubock\", email=\"lubock.nathan@gmail.com\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-8064-2465\")),\nperson(\"Michael\", \"Love\", email=\"michaelisaiahlove@gmail.com\", role = \"ctb\"))", "Description": "Fit linear models to overdispersed count data. The package\ncan estimate the overdispersion and fit repeated models for\nmatrix input. It is designed to handle large input datasets as\nthey typically occur in single cell RNA-seq experiments.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "SystemRequirements": "C++17", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "URL": "https://github.com/const-ae/glmGamPoi", "BugReports": "https://github.com/const-ae/glmGamPoi/issues", "biocViews": "Regression, RNASeq, Software, SingleCell", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-26 21:40:39 UTC", "RemoteUrl": "https://github.com/bioc/glmGamPoi", "RemoteRef": "HEAD", "RemoteSha": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-27 07:11:48 UTC", "User": "root" }, "Author": "Constantin Ahlmann-Eltze [aut, cre] (ORCID:\n),\nNathan Lubock [ctb] (ORCID: ),\nMichael Love [ctb]", "Maintainer": "Constantin Ahlmann-Eltze ", "MD5sum": "bbada23c084aa5451046012a843a29f6", "_user": "bioc", "_type": "src", "_file": "glmGamPoi_1.25.1.tar.gz", "_fileid": "0988ce8371d632931cde09afb56b1fce9a2b9cdde31ae521bd15d6c8d56bac8a", "_filesize": 1994198, "_sha256": "0988ce8371d632931cde09afb56b1fce9a2b9cdde31ae521bd15d6c8d56bac8a", "_created": "2026-05-27T07:11:48.000Z", "_published": "2026-05-27T07:32:44.582Z", "_jobs": [ { "job": 78026162589, "time": 258, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7234186680" }, { "job": 78026162687, "time": 326, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7234208368" }, { "job": 78026162647, "time": 382, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7234225569" }, { "job": 78026162639, "time": 339, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7234211990" }, { "job": 78026162660, "time": 377, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7234224079" }, { "job": 78026162622, "time": 229, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7234349970" }, { "job": 78026162697, "time": 400, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7234271321" }, { "job": 78026162629, "time": 248, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7234324119" }, { "job": 78026162655, "time": 449, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7234293873" }, { "job": 78024855001, "time": 578, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7234114083" }, { "job": 78026162606, "time": 217, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7234174606" }, { "job": 78026162770, "time": 1184, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7234470168" }, { "job": 78026162631, "time": 957, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7234399471" }, { "job": 78026162715, "time": 903, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7234382374" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/glmGamPoi", "_commit": { "id": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "author": "const-ae ", "committer": "const-ae ", "message": "Update NEWS\n", "time": 1779831639 }, "_maintainer": { "name": "Constantin Ahlmann-Eltze", "email": "artjom31415@googlemail.com", "login": "const-ae", "bluesky": "@const-ae.bsky.social", "orcid": "0000-0002-3762-068X", "description": "Postdoc, Biostats, R", "uuid": 5359014 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "beachmat", "role": "LinkingTo" }, { "package": "assorthead", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "beachmat", "role": "Imports" }, { "package": "DelayedMatrixStats", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "SparseArray", "version": ">= 1.5.21", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "HDF5Array", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "zoo", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "statmod", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "bench", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "TENxPBMCData", "role": "Suggests" }, { "package": "muscData", "role": "Suggests" }, { "package": "scran", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 4, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-22", "n": 4 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "regression", "rnaseq", "software", "singlecell", "gamma-poisson", "glm", "negative-binomial-regression", "on-disk", "openblas", "cpp" ], "_stars": 122, "_contributors": [ { "user": "const-ae", "count": 503, "uuid": 5359014 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "nlubock", "count": 4, "uuid": 7013294 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "jackkamm", "count": 1, "uuid": 9089216 }, { "user": "jeffreypullin", "count": 1, "uuid": 34267114 }, { "user": "ltla", "count": 1, "uuid": 8166669 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 10126, "source": "https://www.bioconductor.org/packages/stats/bioc/glmGamPoi" }, "_mentions": 2, "_devurl": "https://github.com/const-ae/glmgampoi", "_searchresults": 2120, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/glmGamPoi.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/const-ae/glmgampoi", "_realowner": "bioc", "_cranurl": false, "_exports": [ "glm_gp", "loc_median_fit", "overdispersion_mle", "overdispersion_shrinkage", "pseudobulk", "test_de", "vars" ], "_help": [ { "page": "as.list.glmGamPoi", "title": "Convert glmGamPoi object to a list", "topics": [ "as.list.glmGamPoi" ] }, { "page": "glm_gp", "title": "Fit a Gamma-Poisson Generalized Linear Model", "topics": [ "glm_gp" ] }, { "page": "loc_median_fit", "title": "Estimate local median fit", "topics": [ "loc_median_fit" ] }, { "page": "overdispersion_mle", "title": "Estimate the Overdispersion for a Vector of Counts", "topics": [ "overdispersion_mle" ] }, { "page": "overdispersion_shrinkage", "title": "Shrink the overdispersion estimates", "topics": [ "overdispersion_shrinkage" ] }, { "page": "predict.glmGamPoi", "title": "Predict 'link' or 'response' values for Gamma-Poisson GLMs", "topics": [ "predict.glmGamPoi" ] }, { "page": "print.glmGamPoi", "title": "Pretty print the result from glm_gp()", "topics": [ "format.glmGamPoi", "format.summary.glmGamPoi", "print.glmGamPoi", "print.summary.glmGamPoi", "summary.glmGamPoi" ] }, { "page": "pseudobulk", "title": "Create a 'SingleCellExperiment' containing pseudo-bulk samples", "topics": [ "pseudobulk" ] }, { "page": "residuals.glmGamPoi", "title": "Extract Residuals of Gamma Poisson Model", "topics": [ "residuals.glmGamPoi" ] }, { "page": "solve_lm_for_A", "title": "Solve the equation Y = A B for A or B", "topics": [ "solve_lm_for_A", "solve_lm_for_B" ] }, { "page": "test_de", "title": "Test for Differential Expression", "topics": [ "test_de" ] }, { "page": "vars", "title": "Quote grouping variables", "topics": [ "vars" ] } ], "_pkglogo": "https://github.com/bioc/glmGamPoi/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/bioc/glmGamPoi/raw/HEAD/README.md", "_rundeps": [ "abind", "assorthead", "beachmat", "Biobase", "BiocGenerics", "biocmake", "cli", "DelayedArray", "DelayedMatrixStats", "dir.expiry", "filelock", "generics", "GenomicRanges", "glue", "h5mread", "HDF5Array", "IRanges", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "RcppArmadillo", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "sparseMatrixStats", "SummarizedExperiment", "vctrs", "XVector" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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": "glmGamPoi.Rmd", "filename": "glmGamPoi.html", "title": "glmGamPoi Quickstart", "author": "Constantin Ahlmann-Eltze", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Example", "Benchmark", "Scalability", "Differential expression analysis", "Session Info" ], "created": "2020-03-27 14:56:30", "modified": "2020-11-17 11:43:58", "commits": 9 }, { "source": "pseudobulk.Rmd", "filename": "pseudobulk.html", "title": "Pseudobulk and differential expression", "author": "Constantin Ahlmann-Eltze", "engine": "knitr::rmarkdown", "headings": [ "Pseudobulk", "Example", "Legacy" ], "created": "2023-01-03 18:08:01", "modified": "2023-02-27 18:11:04", "commits": 5 } ], "_score": 12.120564151099847, "_indexed": true, "_nocasepkg": "glmgampoi", "_universes": [ "bioc", "const-ae" ], "_previous": "1.25.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.1", "date": "2026-05-27T07:15:45.000Z", "distro": "noble", "arch": "aarch64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "da95164dbad10bad87f1ee2f3c35bb6b6d04d6bdeb037f54095477b2364eb525", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.7.0", "os": "linux", "version": "1.25.1", "date": "2026-05-27T07:16:20.000Z", "distro": "noble", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "c1e3464513a413251d0ce1466b0d662bc4ca0aea6073988efde5d4a857d8ce01", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "linux", "version": "1.25.1", "date": "2026-05-27T07:15:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "b1ad92e7a9dc0780ff3889f43ac583533c33e83da786bae7bc2ae2c5a37372a2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "linux", "version": "1.25.1", "date": "2026-05-27T07:16:16.000Z", "distro": "noble", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "f3c8a24e5f133e8613cbd9dc42503728efe169b862a478e4cb135635f6eaf9c3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.5.3", "os": "mac", "version": "1.25.1", "date": "2026-05-27T07:23:54.000Z", "arch": "aarch64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "f0c56777ddecac998c7b78024c93f1d5ea21ac09f22d53dfa998cf95d611a8ae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.5.3", "os": "mac", "version": "1.25.1", "date": "2026-05-27T07:18:09.000Z", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "c61d9eef0cc723bbb1ca5df954ea2b1c0622c561027d7127b6e6c71d95080e2b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "mac", "version": "1.25.1", "date": "2026-05-27T07:22:17.000Z", "arch": "aarch64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "20495a610f64cc1f1371f7c2d45e9505c21d984840b989341a8431d0cece4527", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "mac", "version": "1.25.1", "date": "2026-05-27T07:18:48.000Z", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "ceab2863b7b564febda15cfa5fa8a23eb5886943cd2b3286cca11901e6841387", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.1", "date": "2026-05-27T07:15:55.000Z", "arch": "emscripten", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "fc90e1f1663f9e883df65b2c1b6827b8b672d0692dd3a008eb6b4dc7eeccc6f3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.7.0", "os": "win", "version": "1.25.1", "date": "2026-05-27T07:27:55.000Z", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "74fd5e8cfb4eabb65f37a28981e9c91085973ba72f8a7b0f9081a71ac308fcbe", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.5.3", "os": "win", "version": "1.25.1", "date": "2026-05-27T07:25:02.000Z", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "d07cd9a1cc4826cb12383206a9bd95eb947c0b990cfae5306030ceba720af53b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" }, { "r": "4.6.0", "os": "win", "version": "1.25.1", "date": "2026-05-27T07:24:46.000Z", "arch": "x86_64", "commit": "95cffb79b02ce1239112d3c8b4adabfb448940bf", "fileid": "9adc0109d96690bca7588ed9f3cbd8c00a811f25144f5c4fbaada1df0a6a9e6a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26496172299" } ] }