{ "_id": "6a49430e18cdde069385e98f", "Package": "aggregateBioVar", "Type": "Package", "Title": "Differential Gene Expression Analysis for Multi-subject\nscRNA-seq", "Version": "1.23.0", "Authors@R": "c(\nperson(given = \"Jason\", family = \"Ratcliff\",\nemail = \"jason-ratcliff@uiowa.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7079-334X\")),\nperson(given = \"Andrew\", family = \"Thurman\",\nemail = \"andrew.thurman2@gmail.com\", role = \"aut\"),\nperson(given = \"Michael\", family = \"Chimenti\",\nemail = \"michael-chimenti@uiowa.edu\", role = \"ctb\"),\nperson(given = \"Alejandro\", family = \"Pezzulo\",\nemail = \"alejandro-pezzulo@uiowa.edu\", role = \"ctb\")\n)", "URL": "https://github.com/jasonratcliff/aggregateBioVar", "BugReports": "https://github.com/jasonratcliff/aggregateBioVar/issues", "Description": "For single cell RNA-seq data collected from more than one\nsubject (e.g. biological sample or technical replicates), this\npackage contains tools to summarize single cell gene expression\nprofiles at the level of subject. A SingleCellExperiment object\nis taken as input and converted to a list of\nSummarizedExperiment objects, where each list element\ncorresponds to an assigned cell type. The SummarizedExperiment\nobjects contain aggregate gene-by-subject count matrices and\ninter-subject column metadata for individual subjects that can\nbe processed using downstream bulk RNA-seq tools.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "biocViews": "Software, SingleCell, RNASeq, Transcriptomics,\nTranscription, GeneExpression, DifferentialExpression", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:50 UTC", "RemoteUrl": "https://github.com/bioc/aggregateBioVar", "RemoteRef": "HEAD", "RemoteSha": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 11:42:11 UTC", "User": "root" }, "Author": "Jason Ratcliff [aut, cre] (ORCID:\n),\nAndrew Thurman [aut],\nMichael Chimenti [ctb],\nAlejandro Pezzulo [ctb]", "Maintainer": "Jason Ratcliff ", "_user": "bioc", "_type": "src", "_file": "aggregateBioVar_1.23.0.tar.gz", "_fileid": "https://r2.ropensci.org/85e255d94348e36dd693702804cddc45da679b2dca0fadca8471837b0d16db2e", "_filesize": 1182235, "_sha256": "85e255d94348e36dd693702804cddc45da679b2dca0fadca8471837b0d16db2e", "_expires": "2026-10-12T17:29:49.000Z", "_created": "2026-07-04T11:42:11.000Z", "_published": "2026-07-04T17:29:50.975Z", "_bioccheck": { "error": 0, "warning": 0, "note": 3 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762", "_status": "success", "_upstream": "https://github.com/bioc/aggregateBioVar", "_commit": { "id": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380830 }, "_maintainer": { "name": "Jason Ratcliff", "email": "jason-ratcliff@uiowa.edu", "orcid": "0000-0001-7079-334X" }, "_distro": "resolute", "_jobs": [ { "job": 85152323798, "time": 229, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8081390185" }, { "job": 85152323699, "time": 304, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8081398495" }, { "job": 85152324004, "time": 305, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8081398733" }, { "job": 85152323814, "time": 145, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8081380812" }, { "job": 85152323970, "time": 157, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8081382041" }, { "job": 85152323765, "time": 256, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8081365398" }, { "job": 85152323931, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8081384252" }, { "job": 85152323896, "time": 214, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8081388441" }, { "job": 85152323972, "time": 205, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8081387687" }, { "job": 85152323966, "time": 204, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8081387480" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "magick", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "ggtext", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "singlecell", "rnaseq", "transcriptomics", "transcription", "geneexpression", "differentialexpression" ], "_stars": 5, "_contributors": [ { "user": "jasonratcliff", "count": 3, "uuid": 10624592 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/jasonratcliff/aggregatebiovar", "_searchresults": 19, "_rbuild": "4.6.1", "_assets": [ "extra/aggregateBioVar.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jasonratcliff/aggregatebiovar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateBioVar", "countsByCell", "countsBySubject", "scSubjects", "subjectMetaData", "summarizedCounts" ], "_datasets": [ { "name": "small_airway", "title": "Small Airway 'SingleCellExperiment' object", "object": "small_airway", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "aggregateBioVar", "title": "Aggregate subject-level biological variation", "topics": [ "aggregateBioVar" ] }, { "page": "countsByCell", "title": "Within cell type gene-by-subject matrices", "topics": [ "countsByCell" ] }, { "page": "countsBySubject", "title": "Gene-by-subject count matrix", "topics": [ "countsBySubject" ] }, { "page": "scSubjects", "title": "SingleCellExperiment subject values", "topics": [ "scSubjects" ] }, { "page": "small_airway", "title": "Small Airway 'SingleCellExperiment' object", "topics": [ "small_airway" ] }, { "page": "subjectMetaData", "title": "Collate metadata variation", "topics": [ "subjectMetaData" ] }, { "page": "summarizedCounts", "title": "Aggregate feature counts and metadata by subject", "topics": [ "summarizedCounts" ] } ], "_readme": "https://github.com/bioc/aggregateBioVar/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "DelayedArray", "generics", "GenomicRanges", "glue", "IRanges", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "SummarizedExperiment", "tibble", "utf8", "vctrs", "XVector" ], "_vignettes": [ { "source": "multi-subject-scRNA-seq.Rmd", "filename": "multi-subject-scRNA-seq.html", "title": "Multi-subject scRNA-seq Analysis", "author": "Jason Ratcliff, Andrew Thurman, Michael Chimenti, Alejandro Pezzulo", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Case Study: Small Airway Epithelium in Cystic Fibrosis", "The small_airway Dataset", "Cell Metadata", "Aggregating Gene Counts", "Gene-by-subject Count Matrix", "Subject Metadata", "Return SummarizedExperiment", "aggregateBioVar()", "Application to Differential Gene Expression (DGE)", "Exploratory Data Analysis", "DGE with DESeq2", "Results", "References", "Session Info" ], "created": "2020-09-03 16:37:14", "modified": "2020-09-03 16:37:14", "commits": 1 } ], "_score": 5.153814864344529, "_indexed": true, "_nocasepkg": "aggregatebiovar", "_universes": [ "bioc", "jasonratcliff" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-07-04T11:45:39.000Z", "distro": "resolute", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/f1afb6b747954d0553e5c9734478d3c1c24a633b64b456ed21dbcf61ff80ee89", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.6.1", "os": "linux", "version": "1.23.0", "date": "2026-07-04T11:45:36.000Z", "distro": "resolute", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/a4db383f2ce34d84db615070881c613517b562d3ed72ce070078bdc7c3ee8e04", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-07-04T11:43:48.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/01ce6cbe7d71b7bca2b37dc15b7f278e3ec9e4c63542bb69b3c43791bb756e86", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.6.1", "os": "mac", "version": "1.23.0", "date": "2026-07-04T11:44:02.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/27769be5378f60ee192ba7c5c906b09d550eadcdf6a4a5736af93d1c53fd2952", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-07-04T11:45:35.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/65268e531fd4f63a4f047db03e69da08d06683a585c2bc34e42ccb8ee81e4d75", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-07-04T11:44:02.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/092cff653b430fed43ecdd94a31d17819c24a597a0e44ce4e64ecdae54e486e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-07-04T11:44:03.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/174eeffe6c32fc8114b593078f828cc9984b6f2a034f22878cc76a017aaa9467", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" }, { "r": "4.6.1", "os": "win", "version": "1.23.0", "date": "2026-07-04T11:44:00.000Z", "commit": "b5448dbe62f6e6b41d78d1f864567ffb7bea6798", "fileid": "https://r2.ropensci.org/8f9f6184fd2f6023763cc16ae02da5a931d3bf446c7db3993a023b3accc79a21", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28704993762" } ] }