{ "_id": "6a193df8acfb0bcc41dd57d2", "Package": "IgGeneUsage", "Type": "Package", "Title": "Differential gene usage in immune repertoires", "Version": "1.26.0", "Authors@R": "person(given = \"Simo\",\nfamily = \"Kitanovski\",\nrole = c(\"aut\", \"cre\"),\nemail = \"simo.kitanovski@uni-due.de\")", "Description": "Detection of biases in the usage of immunoglobulin (Ig)\ngenes is an important task in immune repertoire profiling.\nIgGeneUsage detects aberrant Ig gene usage between biological\nconditions using a probabilistic model which is analyzed\ncomputationally by Bayes inference. With this IgGeneUsage also\navoids some common problems related to the current practice of\nnull-hypothesis significance testing.", "License": "MIT + file LICENSE", "SystemRequirements": "GNU make", "Encoding": "UTF-8", "LazyData": "false", "NeedsCompilation": "yes", "biocViews": "DifferentialExpression, Regression, Genetics, Bayesian,\nBiomedicalInformatics, ImmunoOncology, MathematicalBiology", "BugReports": "https://github.com/snaketron/IgGeneUsage/issues", "URL": "https://github.com/snaketron/IgGeneUsage", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "Biarch": "true", "Config/pak/sysreqs": "make libicu-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:50:40 UTC", "RemoteUrl": "https://github.com/bioc/IgGeneUsage", "RemoteRef": "RELEASE_3_23", "RemoteSha": "08fbf3746498b3525fb8f377c33f49949167673b", "Packaged": { "Date": "2026-05-29 06:14:17 UTC", "User": "root" }, "Author": "Simo Kitanovski [aut, cre]", "Maintainer": "Simo Kitanovski ", "MD5sum": "a49d4cd41222b4a9ee98f2baac4ad662", "_user": "bioc-release", "_type": "src", "_file": "IgGeneUsage_1.26.0.tar.gz", "_fileid": "f075035c4ecbec18cd1e917eba059ec802c5e754236f1dbad391843bedc5a3bd", "_filesize": 1286377, "_sha256": "f075035c4ecbec18cd1e917eba059ec802c5e754236f1dbad391843bedc5a3bd", "_created": "2026-05-29T06:14:17.000Z", "_published": "2026-05-29T07:19:20.261Z", "_jobs": [ { "job": 78448617244, "time": 442, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7284470253" }, { "job": 78448617273, "time": 801, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7284553270" }, { "job": 78448617243, "time": 910, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7284580819" }, { "job": 78448617291, "time": 795, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7284551793" }, { "job": 78448617275, "time": 896, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7284577185" }, { "job": 78448617341, "time": 497, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7284952847" }, { "job": 78448617413, "time": 1620, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7285229061" }, { "job": 78448617260, "time": 486, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7284949671" }, { "job": 78448617365, "time": 1264, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7285140532" }, { "job": 78446862330, "time": 944, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284367073" }, { "job": 78448617278, "time": 168, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78448617237, "time": 1267, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7284664303" }, { "job": 78448617309, "time": 867, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7284572151" }, { "job": 78448617242, "time": 1020, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7284607286" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/IgGeneUsage", "_commit": { "id": "08fbf3746498b3525fb8f377c33f49949167673b", "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": 1777380640 }, "_maintainer": { "name": "Simo Kitanovski", "email": "simo.kitanovski@uni-due.de", "login": "snaketron", "description": "", "uuid": 5060977 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "BH", "version": ">= 1.66.0", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.18.1", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.18.0", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "reshape2", "version": ">= 1.4.3", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "Imports" }, { "package": "rstan", "version": ">= 2.18.1", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.2.0", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "ggforce", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "differentialexpression", "regression", "genetics", "bayesian", "biomedicalinformatics", "immunooncology", "mathematicalbiology", "b-cell-receptor", "bcr-repertoire", "differential-analysis", "differential-gene-expression", "high-throughput-sequencing", "immune-repertoire", "immune-repertoire-analysis", "immune-repertoires", "immunogenomics", "immunoglobulin", "immunoinformatics", "immunological-bioinformatics", "immunology", "tcr-repertoire", "vdj-recombination", "cpp" ], "_stars": 6, "_contributors": [ { "user": "snaketron", "count": 546, "uuid": 5060977 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 332, "source": "https://www.bioconductor.org/packages/stats/bioc/IgGeneUsage" }, "_devurl": "https://github.com/snaketron/iggeneusage", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/IgGeneUsage.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/snaketron/iggeneusage", "_realowner": "bioc", "_cranurl": false, "_exports": [ "DGU", "LOO" ], "_datasets": [ { "name": "CDR3_Epitopes", "title": "Net charge usage in CDR3 sequences of T-cell receptor repertoires disturbed by Influenza-A and CMV", "object": "CDR3_Epitopes", "file": "CDR3_Epitopes.RData", "class": [ "data.frame" ], "fields": [ "condition", "gene_name", "gene_usage_count", "individual_id" ], "rows": 143, "table": true, "tojson": true }, { "name": "d_zibb_1", "title": "Simulated Ig gene usage data", "object": "d_zibb_1", "file": "d_zibb_1.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "condition", "gene_name", "gene_usage_count" ], "rows": 75, "table": true, "tojson": true }, { "name": "d_zibb_2", "title": "Simulated Ig gene usage data", "object": "d_zibb_2", "file": "d_zibb_2.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "condition", "gene_name", "replicate", "gene_usage_count" ], "rows": 225, "table": true, "tojson": true }, { "name": "d_zibb_3", "title": "Simulated Ig gene usage data", "object": "d_zibb_3", "file": "d_zibb_3.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "gene_name", "gene_usage_count", "condition" ], "rows": 120, "table": true, "tojson": true }, { "name": "d_zibb_4", "title": "Simulated Ig gene usage data", "object": "d_zibb_4", "file": "d_zibb_4.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "condition", "gene_name", "replicate", "gene_usage_count" ], "rows": 320, "table": true, "tojson": true }, { "name": "d_zibb_5", "title": "Simulated Ig gene usage data", "object": "d_zibb_5", "file": "d_zibb_5.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "condition", "gene_name", "gene_usage_count" ], "rows": 180, "table": true, "tojson": true }, { "name": "d_zibb_6", "title": "Simulated Ig gene usage data", "object": "d_zibb_6", "file": "d_zibb_6.RData", "class": [ "data.frame" ], "fields": [ "individual_id", "condition", "gene_name", "replicate", "gene_usage_count" ], "rows": 1080, "table": true, "tojson": true }, { "name": "Ig", "title": "IGHV gene family usage in vaccine-challenged B-cell repertoires", "object": "Ig", "file": "Ig.RData", "class": [ "data.frame" ], "fields": [ "gene_name", "condition", "gene_usage_count", "individual_id" ], "rows": 48, "table": true, "tojson": true }, { "name": "Ig_SE", "title": "IGHV gene family usage in vaccine-challenged B-cell repertoires (SummarizedExperiment object)", "object": "Ig_SE", "file": "Ig_SE.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "IGHV_HCV", "title": "IGHV gene usage in HCV+ and healthy individuals", "object": "IGHV_HCV", "file": "IGHV_HCV.RData", "class": [ "data.frame" ], "fields": [ "condition", "gene_name", "gene_usage_count", "individual_id" ], "rows": 2001, "table": true, "tojson": true } ], "_help": [ { "page": "IgGeneUsage-package", "title": "The R package IgGeneUsage", "topics": [ "IgGeneUsage-package", "IgGeneUsage" ] }, { "page": "IGHV_Epitopes", "title": "Net charge usage in CDR3 sequences of T-cell receptor repertoires disturbed by Influenza-A and CMV", "topics": [ "CDR3_Epitopes" ] }, { "page": "d_zibb_1", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_1" ] }, { "page": "d_zibb_2", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_2" ] }, { "page": "d_zibb_3", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_3" ] }, { "page": "d_zibb_4", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_4" ] }, { "page": "d_zibb_5", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_5" ] }, { "page": "d_zibb_6", "title": "Simulated Ig gene usage data", "topics": [ "d_zibb_6" ] }, { "page": "DGU", "title": "Differential immunoglobulin (Ig) gene usage in immune repertoires", "topics": [ "DGU" ] }, { "page": "Ig", "title": "IGHV gene family usage in vaccine-challenged B-cell repertoires", "topics": [ "Ig" ] }, { "page": "Ig_SE", "title": "IGHV gene family usage in vaccine-challenged B-cell repertoires (SummarizedExperiment object)", "topics": [ "Ig_SE" ] }, { "page": "IGHV_HCV", "title": "IGHV gene usage in HCV+ and healthy individuals", "topics": [ "IGHV_HCV" ] }, { "page": "LOO", "title": "Leave-one-out analysis for quantitative evaluation of the probability of DGU", "topics": [ "LOO" ] } ], "_readme": "https://github.com/bioc/IgGeneUsage/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "backports", "BH", "Biobase", "BiocGenerics", "callr", "checkmate", "cli", "cpp11", "DelayedArray", "desc", "distributional", "dplyr", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "inline", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "numDeriv", "pillar", "pkgbuild", "pkgconfig", "plyr", "posterior", "processx", "ps", "purrr", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "reshape2", "rlang", "rstan", "rstantools", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "StanHeaders", "stringi", "stringr", "SummarizedExperiment", "tensorA", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "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": "User_Manual.Rmd", "filename": "User_Manual.html", "title": "User Manual: IgGeneUsage", "author": "SK", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Input", "Model", "Case Study A: analyzing IRRs", "DGU analysis", "Output format", "Model checking", "MCMC sampling", "PPC: posterior predictive checks", "PPCs: repertoire-specific", "PPCs: overall", "Results", "DGU: differential gene usage", "Promising hits", "Promising hits [count]", "GU: gene usage summary", "Leave-one-out (LOO) analysis", "LOO-DGU: variability of effect size $\\gamma$", "LOO-DGU: variability of $\\pi$", "LOO-GU: variability of the gene usage", "Case Study B: analyzing IRRs containing biological replicates", "Modeling", "Posterior predictive checks", "Analysis of estimated effect sizes", "Session" ], "created": "2022-10-17 21:43:58", "modified": "2024-04-05 15:17:57", "commits": 23 } ], "_score": 5.380211241711606, "_indexed": false, "_nocasepkg": "iggeneusage", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/IgGeneUsage", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-05-29T06:21:35.000Z", "distro": "noble", "arch": "aarch64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "db136a3d37426414322e8997c5ee18cea0d0b69553ff0575c0448455c7149301", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.7.0", "os": "linux", "version": "1.26.0", "date": "2026-05-29T06:22:17.000Z", "distro": "noble", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "fa79d88de8d1c47ef44d3a1f0b900d7095e3eca59bac1ea2579d6a86ccb8fcb0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.6.0", "os": "linux", "version": "1.26.0", "date": "2026-05-29T06:21:23.000Z", "distro": "noble", "arch": "aarch64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "50c1b6b9c3d94318313b1ef95d61a8c24bd1cba34ba9b1ebe5dfaeaf16a7d440", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.6.0", "os": "linux", "version": "1.26.0", "date": "2026-05-29T06:21:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "097d1f67776a1c613e1390951d91baa604ea15509a384943667f2126960ae0d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.5.3", "os": "mac", "version": "1.26.0", "date": "2026-05-29T06:53:41.000Z", "arch": "aarch64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "1c33e2979da7ed7152bba06e391cfed7b6908aa1c076ef5f30adfaa396fe9518", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.5.3", "os": "mac", "version": "1.26.0", "date": "2026-05-29T06:56:08.000Z", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "16bf63a7dce382b90dab1ae8a6656e7f279a5e66bc5457a2384e56125c1ad4ff", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.6.0", "os": "mac", "version": "1.26.0", "date": "2026-05-29T06:53:55.000Z", "arch": "aarch64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "e057669dbd45ba32c54e33ce8117471e4722e28b303770e72764b39dd199b7d1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.6.0", "os": "mac", "version": "1.26.0", "date": "2026-05-29T06:55:34.000Z", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "15dfd2c20df17e8815d737d3986618b44dc69ff5bcc7b8e28a930db95ecf01b1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.7.0", "os": "win", "version": "1.26.0", "date": "2026-05-29T06:20:42.000Z", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "3affcdbd84105eaa5b79753ad09bad2025eb4944cb1aebedfc613b9a3afcdede", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.5.3", "os": "win", "version": "1.26.0", "date": "2026-05-29T06:21:50.000Z", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "385126733c5ff0d2f697f84a89bf234ec82dd0c538f5bab7b1eb4f186b0bb281", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" }, { "r": "4.6.0", "os": "win", "version": "1.26.0", "date": "2026-05-29T06:20:21.000Z", "arch": "x86_64", "commit": "08fbf3746498b3525fb8f377c33f49949167673b", "fileid": "ccc9af0c891f47bb7b74503b035e47ef2722d83d84abf0692b858d7da5bf9785", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621055677" } ] }