{ "_id": "6ac4d228f511ae58c09a1db2", "Package": "countsimQC", "Type": "Package", "Title": "Compare Characteristic Features of Count Data Sets", "Version": "1.30.0", "Authors@R": "c(person(\"Charlotte\", \"Soneson\", role = c(\"aut\", \"cre\"), \nemail = \"charlottesoneson@gmail.com\", comment = c(ORCID = \"0000-0003-3833-2169\")))", "Description": "countsimQC provides functionality to create a\ncomprehensive report comparing a broad range of characteristics\nacross a collection of count matrices. One important use case\nis the comparison of one or more synthetic count matrices to a\nreal count matrix, possibly the one underlying the simulations.\nHowever, any collection of count matrices can be compared.", "License": "GPL (>=2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "Microbiome, RNASeq, SingleCell, ExperimentalDesign,\nQualityControl, ReportWriting, Visualization, ImmunoOncology", "URL": "https://github.com/csoneson/countsimQC", "BugReports": "https://github.com/csoneson/countsimQC/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:48:48 UTC", "RemoteUrl": "https://github.com/bioc/countsimQC", "RemoteRef": "RELEASE_3_23", "RemoteSha": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-06 10:38:40 UTC", "User": "root" }, "Author": "Charlotte Soneson [aut, cre] (ORCID:\n)", "Maintainer": "Charlotte Soneson ", "_user": "bioc-release", "_type": "src", "_file": "countsimQC_1.30.0.tar.gz", "_fileid": "https://r2.ropensci.org/cebe6fb8e9970a69f7d51819e2f70d8f378327f802c11fdf755201f1dedf6ed6", "_filesize": 551147, "_sha256": "cebe6fb8e9970a69f7d51819e2f70d8f378327f802c11fdf755201f1dedf6ed6", "_expires": "2027-01-14T10:49:10.000Z", "_created": "2026-10-06T10:38:40.000Z", "_published": "2026-10-06T10:49:12.584Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159", "_status": "success", "_upstream": "https://github.com/bioc/countsimQC", "_commit": { "id": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "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": 1777380528 }, "_maintainer": { "name": "Charlotte Soneson", "email": "charlottesoneson@gmail.com", "login": "csoneson", "orcid": "0000-0003-3833-2169", "description": "", "uuid": 5628952 }, "_distro": "resolute", "_jobs": [ { "job": 112227974665, "time": 173, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11406303440" }, { "job": 112227974662, "time": 505, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11405179939" }, { "job": 112227974690, "time": 571, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11406924296" }, { "job": 112227974716, "time": 384, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11405344556" }, { "job": 112227974737, "time": 372, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11406418845" }, { "job": 112225905541, "time": 342, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11406257897" }, { "job": 112227974687, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11406813111" }, { "job": 112227974826, "time": 439, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11405184810" }, { "job": 112227974709, "time": 370, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11406728480" }, { "job": 112227974797, "time": 288, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11405249241" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "rmarkdown", "version": ">= 2.5", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "DESeq2", "version": ">= 1.16.0", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "genefilter", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "GenomeInfoDbData", "role": "Imports" }, { "package": "caTools", "role": "Imports" }, { "package": "randtests", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "ragg", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 1 }, { "week": "2026-06", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.31.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.30.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "microbiome", "rnaseq", "singlecell", "experimentaldesign", "qualitycontrol", "reportwriting", "visualization", "immunooncology" ], "_stars": 31, "_contributors": [ { "user": "csoneson", "count": 197, "uuid": 5628952 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "kant", "count": 1, "uuid": 32717 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 473, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1048, "source": "https://www.bioconductor.org/packages/stats/bioc/countsimQC" }, "_mentions": 6, "_devurl": "https://github.com/csoneson/countsimqc", "_searchresults": 42, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/countsimQC.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/csoneson/countsimqc", "_realowner": "bioc", "_cranurl": false, "_exports": [ "countsimQCReport", "generateIndividualPlots" ], "_datasets": [ { "name": "countsimExample", "title": "Example list with three count data sets", "object": "countsimExample", "file": "countsimExample.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "countsimExample_dfmat", "title": "Example list with three count data sets in different formats", "object": "countsimExample_dfmat", "file": "countsimExample_dfmat.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "countsimExample", "title": "Example list with three count data sets", "topics": [ "countsimExample" ] }, { "page": "countsimExample_dfmat", "title": "Example list with three count data sets in different formats", "topics": [ "countsimExample_dfmat" ] }, { "page": "countsimQCReport", "title": "Generate countsimQC report", "topics": [ "countsimQCReport" ] }, { "page": "generateIndividualPlots", "title": "Generate individual plots from countsimQCReport output", "topics": [ "generateIndividualPlots" ] } ], "_readme": "https://github.com/bioc/countsimQC/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "cachem", "caTools", "cli", "codetools", "cpp11", "crayon", "crosstalk", "curl", "DBI", "DelayedArray", "DESeq2", "digest", "dplyr", "DT", "edgeR", "evaluate", "farver", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "genefilter", "generics", "GenomeInfoDbData", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "otel", "pillar", "pkgconfig", "png", "promises", "purrr", "R6", "ragg", "randtests", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml" ], "_vignettes": [ { "source": "countsimQC.Rmd", "filename": "countsimQC.html", "title": "countsimQC - Comparing characteristic features across count data sets", "author": "Charlotte Soneson", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Data preparation", "Report generation", "Generation of individual figures", "Input data format", "Session info" ], "created": "2017-05-15 18:29:50", "modified": "2020-04-19 11:46:13", "commits": 13 } ], "_score": 7.788184780655225, "_indexed": false, "_nocasepkg": "countsimqc", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/countsimQC", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.30.0", "date": "2026-10-06T10:42:24.000Z", "distro": "resolute", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/7c730f8283e2a637b8394ef1a88ca44152c5f672d3655987aa6c1a473f14822c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.6.1", "os": "linux", "version": "1.30.0", "date": "2026-10-06T10:43:37.000Z", "distro": "resolute", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/cf426fe690357363d8896b4c8e390c3b4adf4a233ffac20153c8801644bb8071", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.5.3", "os": "mac", "version": "1.30.0", "date": "2026-10-06T10:41:17.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/ca7bbe59279accaa4f4433e7e91ade4a34ec7a28defe61b7cfc3e4243780a8a8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.6.1", "os": "mac", "version": "1.30.0", "date": "2026-10-06T10:42:18.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/0cd3bf1986244f01e45b1459c27226b54918c43e91ccdba364490b467432de96", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.6.0", "os": "wasm", "version": "1.30.0", "date": "2026-10-06T10:41:45.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/d3e292c1a098d2cd87d0c9b36209b298fb7dd709ef92faef8ed8ccc83f4b82d9", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.7.0", "os": "win", "version": "1.30.0", "date": "2026-10-06T10:40:45.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/cda52fffaac030b3ee5e222c93c9695d91820ef433c414b27394f1188019c634", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.5.3", "os": "win", "version": "1.30.0", "date": "2026-10-06T10:40:31.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/3b517ed1897588b3b48236d184c670fc146e2406e1bfed33d492712c004779a0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" }, { "r": "4.6.1", "os": "win", "version": "1.30.0", "date": "2026-10-06T10:40:23.000Z", "commit": "97608e93124e2f5aa7308d2e565ef7c5347d7736", "fileid": "https://r2.ropensci.org/66cafa9cdbe443cf67c6d251b468def20750e5d7efb8ec041fdfe415d800fba9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/37450551159" } ] }