{ "_id": "6ab38ff33d719c1f840913ba", "Package": "qsvaR", "Title": "Generate Quality Surrogate Variable Analysis for Degradation\nCorrection", "Version": "1.16.0", "Date": "2025-09-29", "Authors@R": "c(\nperson(\"Joshua\", \"Stolz\", email = \"jstolz80@gmail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-5694-5247\")),\nperson(\"Hedia\", \"Tnani\", email = \"hediatnani0@gmail.com\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-0380-9740\")),\nperson(\"Leonardo\", \"Collado-Torres\", role = c(\"ctb\"),\nemail = \"lcolladotor@gmail.com\", comment = c(ORCID = \"0000-0003-2140-308X\")),\nperson(\"Nicholas J.\", \"Eagles\", email = \"nickeagles77@gmail.com\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-9808-5254\"))\n)", "Description": "The qsvaR package contains functions for removing the\neffect of degration in rna-seq data from postmortem brain\ntissue. The package is equipped to help users generate\nprincipal components associated with degradation. The\ncomponents can be used in differential expression analysis to\nremove the effects of degradation.", "License": "Artistic-2.0", "URL": "https://github.com/LieberInstitute/qsvaR", "BugReports": "https://support.bioconductor.org/t/qsvaR", "biocViews": "Software, WorkflowStep, Normalization, BiologicalQuestion,\nDifferentialExpression, Sequencing, Coverage", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "LazyData": "true", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:58:04 UTC", "RemoteUrl": "https://github.com/bioc/qsvaR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-23 08:30:00 UTC", "User": "root" }, "Author": "Joshua Stolz [aut] (ORCID: ),\nHedia Tnani [ctb] (ORCID: ),\nLeonardo Collado-Torres [ctb] (ORCID:\n),\nNicholas J. Eagles [aut, cre] (ORCID:\n)", "Maintainer": "Nicholas J. Eagles ", "_user": "bioc-release", "_type": "src", "_file": "qsvaR_1.16.0.tar.gz", "_fileid": "https://r2.ropensci.org/7b9528a854ac9fa95a61be4f3377c6b6553bfc2c9d79f518def3b4d250220656", "_filesize": 3343458, "_sha256": "7b9528a854ac9fa95a61be4f3377c6b6553bfc2c9d79f518def3b4d250220656", "_expires": "2027-01-01T08:38:08.000Z", "_created": "2026-09-23T08:30:00.000Z", "_published": "2026-09-23T08:38:11.023Z", "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274", "_status": "success", "_upstream": "https://github.com/bioc/qsvaR", "_commit": { "id": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "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": 1777381084 }, "_maintainer": { "name": "Nicholas J. Eagles", "email": "nickeagles77@gmail.com", "login": "nick-eagles", "linkedin": "in/nick-eagles-7a5b30161", "orcid": "0000-0002-9808-5254", "description": "Data scientist with strong data engineering expertise, specializing in scalable data pipelines, reproducible analytics, and ML-driven insight generation.", "uuid": 45461721 }, "_distro": "resolute", "_jobs": [ { "job": 107104426204, "time": 246, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10739234469" }, { "job": 107104426110, "time": 424, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10739978154" }, { "job": 107104426225, "time": 432, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10740021634" }, { "job": 107104426166, "time": 182, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "10739629722" }, { "job": 107104426112, "time": 263, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "10740066034" }, { "job": 107102724390, "time": 329, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10739986637" }, { "job": 107104426067, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10739124677" }, { "job": 107104426183, "time": 285, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10739778746" }, { "job": 107104426262, "time": 299, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "10739244631" }, { "job": 107104426153, "time": 252, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10740520143" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "RefManageR", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "software", "workflowstep", "normalization", "biologicalquestion", "differentialexpression", "sequencing", "coverage", "bioconductor", "brain", "degradation", "human", "qsva" ], "_stars": 0, "_contributors": [ { "user": "joshstolz", "count": 168, "uuid": 62106682 }, { "user": "hediatnani", "count": 122, "uuid": 59562743 }, { "user": "lcolladotor", "count": 55, "uuid": 2288213 }, { "user": "gpertea", "count": 19, "uuid": 3372619 }, { "user": "nick-eagles", "count": 19, "uuid": 45461721 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 2, "uuid": 2746443 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 468, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 406, "source": "https://www.bioconductor.org/packages/stats/bioc/qsvaR" }, "_devurl": "https://github.com/lieberinstitute/qsvar", "_searchresults": 10, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/qsvaR.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/lieberinstitute/qsvar", "_realowner": "bioc", "_cranurl": false, "_exports": [ "DEqual", "get_qsvs", "getDegTx", "getPCs", "k_qsvs", "normalize_tx_names", "qSVA", "select_transcripts", "which_tx_names" ], "_datasets": [ { "name": "degradation_tstats", "title": "Degradation time t-statistics", "object": "degradation_tstats", "class": [ "data.frame" ], "fields": [ "t" ], "rows": 45082, "table": true, "tojson": true }, { "name": "rse_tx", "title": "Example of RSE object with RNA-seq transcript quantification data", "object": "rse_tx", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "transcripts", "title": "Transcripts for Degradation Models", "object": "transcripts", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "degradation_tstats", "title": "Degradation time t-statistics", "topics": [ "degradation_tstats" ] }, { "page": "DEqual", "title": "Differential expression quality (DEqual) plot", "topics": [ "DEqual" ] }, { "page": "get_qsvs", "title": "Generate matrix of qsvs", "topics": [ "get_qsvs" ] }, { "page": "getDegTx", "title": "Obtain expression matrix for degraded transcripts", "topics": [ "getDegTx" ] }, { "page": "getPCs", "title": "PCs from transcripts", "topics": [ "getPCs" ] }, { "page": "k_qsvs", "title": "Apply num.sv algorithm to determine the number of pcs to be included", "topics": [ "k_qsvs" ] }, { "page": "normalize_tx_names", "title": "Remove version number from Gencode/Ensembl transcript names", "topics": [ "normalize_tx_names" ] }, { "page": "qSVA", "title": "A wrapper function used to perform qSVA in one step.", "topics": [ "qSVA" ] }, { "page": "rse_tx", "title": "Example of RSE object with RNA-seq transcript quantification data", "topics": [ "rse_tx" ] }, { "page": "select_transcripts", "title": "Select transcripts associated with degradation", "topics": [ "select_transcripts" ] }, { "page": "transcripts", "title": "Transcripts for Degradation Models", "topics": [ "transcripts" ] }, { "page": "which_tx_names", "title": "Check validity of transcript vectors and return a vector matching indexes in tx1", "topics": [ "which_tx_names" ] } ], "_readme": "https://github.com/bioc/qsvaR/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "dplyr", "edgeR", "farver", "fastmap", "formatR", "futile.logger", "futile.options", "genefilter", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "pillar", "pkgconfig", "png", "R6", "RColorBrewer", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "SummarizedExperiment", "survival", "sva", "sys", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "Intro_qsvaR.Rmd", "filename": "Intro_qsvaR.html", "title": "Introduction to qsvaR", "author": "Joshua M. Stolz, Hedia Tnani, Leonardo Collado-Torres", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install qsvaR", "Required knowledge", "Asking for help", "Citing qsvaR", "qsvaR Overview", "Significant Transcripts", "Get Degradation Matrix", "Generate principal components", "Calculate Number of PCs Needed", "Return qSV Matrix", "Differential Expression", "Conclusion", "Acknowledgements", "Reproducibility", "Bibliography" ], "created": "2021-12-14 16:34:57", "modified": "2024-11-26 18:41:15", "commits": 61 } ], "_score": 5.243038048686294, "_indexed": false, "_nocasepkg": "qsvar", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/qsvaR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.16.0", "date": "2026-09-23T08:34:22.000Z", "distro": "resolute", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/c9fb550b8e6e6b739bbde3009dcb319bbb1b4aa89565e5823e7b70a02ba5a550", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.6.1", "os": "linux", "version": "1.16.0", "date": "2026-09-23T08:35:14.000Z", "distro": "resolute", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/82d811ed69351986849f2e609ec49c7093429f8eeec8a57cfc1f43b233d7da75", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.5.3", "os": "mac", "version": "1.16.0", "date": "2026-09-23T08:31:45.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/8765081821f71e30ee1c1cb58fc670fffcc7a89bc5aaf6d7bd5e0fdda403e415", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.6.1", "os": "mac", "version": "1.16.0", "date": "2026-09-23T08:32:11.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/1ca3dcf3c86b03acca7c19413ef1d0fa114b4ddd2fe5e0f16b11f91db97bd2ce", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.6.0", "os": "wasm", "version": "1.16.0", "date": "2026-09-23T08:33:17.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/4c209577d313f36086f64631e6cdd8092f2bff078db991f4948feaefa39ffefd", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.7.0", "os": "win", "version": "1.16.0", "date": "2026-09-23T08:31:42.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/1704b30b75d83cb55f7f2f5631f95ca47dc56354c02169b612c7c213373ea1ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.5.3", "os": "win", "version": "1.16.0", "date": "2026-09-23T08:31:49.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/114c41032a89843edf53993204ffd663e011bd7fb041aedc707886ec0ac00d1f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" }, { "r": "4.6.1", "os": "win", "version": "1.16.0", "date": "2026-09-23T08:31:37.000Z", "commit": "a2ac40ec7b829d42c0a58c91ccfd00aa43b54963", "fileid": "https://r2.ropensci.org/a3ecab7de81382623295552c76500e01774f2d05b25917292caa788063ed2e44", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/35836960274" } ] }