{ "_id": "6a1aee531d7bb097a09f592c", "Package": "msmsTests", "Type": "Package", "Title": "LC-MS/MS Differential Expression Tests", "Version": "1.51.0", "Date": "2013-10-02", "Author": "Josep Gregori, Alex Sanchez, and Josep Villanueva", "Maintainer": "Josep Gregori i Font ", "Description": "Statistical tests for label-free LC-MS/MS data by spectral\ncounts, to discover differentially expressed proteins between\ntwo biological conditions. Three tests are available: Poisson\nGLM regression, quasi-likelihood GLM regression, and the\nnegative binomial of the edgeR package.The three models admit\nblocking factors to control for nuissance variables.To assure a\ngood level of reproducibility a post-test filter is available,\nwhere we may set the minimum effect size considered biologicaly\nrelevant, and the minimum expression of the most abundant\ncondition.", "License": "GPL-2", "biocViews": "ImmunoOncology, Software, MassSpectrometry, Proteomics", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:00 UTC", "RemoteUrl": "https://github.com/bioc/msmsTests", "RemoteRef": "HEAD", "RemoteSha": "36efb3a9419a448d69c5110a2990472703b43e6d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:41:21 UTC", "User": "root" }, "MD5sum": "d20c0dcc55b29c3b674a9efa4a8023cc", "_user": "bioc", "_type": "src", "_file": "msmsTests_1.51.0.tar.gz", "_fileid": "bacd7d0d057ea76ac341a48089a216a106446a142ed215c75ac7914f17a22cd1", "_filesize": 434363, "_sha256": "bacd7d0d057ea76ac341a48089a216a106446a142ed215c75ac7914f17a22cd1", "_created": "2026-05-30T09:41:21.000Z", "_published": "2026-05-30T14:04:03.064Z", "_jobs": [ { "job": 78640339633, "time": 196, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307401373" }, { "job": 78640339619, "time": 373, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307416353" }, { "job": 78640339618, "time": 310, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307411419" }, { "job": 78640339621, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308721808" }, { "job": 78640339620, "time": 174, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308721675" }, { "job": 78639679021, "time": 295, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307256495" }, { "job": 78640339623, "time": 168, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307398041" }, { "job": 78640339632, "time": 245, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307404057" }, { "job": 78640339637, "time": 265, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307406092" }, { "job": 78640339639, "time": 277, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307407881" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/msmsTests", "_commit": { "id": "36efb3a9419a448d69c5110a2990472703b43e6d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379880 }, "_maintainer": { "name": "Josep Gregori i Font", "email": "josep.gregori@gmail.com", "login": "josepgregori", "description": "", "uuid": 6534561 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.1", "role": "Depends" }, { "package": "MSnbase", "role": "Depends" }, { "package": "msmsEDA", "role": "Depends" }, { "package": "edgeR", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "xtable", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "software", "massspectrometry", "proteomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 688, "source": "https://www.bioconductor.org/packages/stats/bioc/msmsTests" }, "_mentions": 4, "_searchresults": 22, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/msmsTests.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "msms.edgeR", "msms.glm.pois", "msms.glm.qlll", "pval.by.fc", "res.volcanoplot", "test.results" ], "_datasets": [ { "name": "msms.spk", "title": "Yeast lisate samples spiked with human proteins", "object": "msms.spk", "file": "msms.spk.rda", "class": [ "MSnSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "msmsTests-package", "title": "LC-MS/MS Differential Expression Tests", "topics": [ "msmsTests-package", "msmsTests" ] }, { "page": "msms.edgeR", "title": "Spectral counts differential expression by edgeR", "topics": [ "msms.edgeR" ] }, { "page": "msms.glm.pois", "title": "Spectral counts differential expression by Poisson GLM", "topics": [ "msms.glm.pois" ] }, { "page": "msms.glm.qlll", "title": "Spectral counts differential expression by quasi-likelihood GLM", "topics": [ "msms.glm.qlll" ] }, { "page": "msms.spk", "title": "Yeast lisate samples spiked with human proteins", "topics": [ "msms.spk" ] }, { "page": "pval.by.fc", "title": "Table of cumulative frequencies of p-values by log fold change bins", "topics": [ "pval.by.fc" ] }, { "page": "res.volcanoplot", "title": "Volcanoplot", "topics": [ "res.volcanoplot" ] }, { "page": "test.results", "title": "Multitest p-value adjustment and post-test filter", "topics": [ "test.results" ] } ], "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bitops", "bslib", "cachem", "caTools", "cli", "clue", "cluster", "codetools", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "edgeR", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gplots", "gtable", "gtools", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "MALDIquant", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "msmsEDA", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "preprocessCore", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "qvalue", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "msmsTests-Vignette2.Rnw", "filename": "msmsTests-Vignette2.pdf", "title": "msmsTests: controlling batch effects by blocking", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:31:38", "modified": "2013-11-01 20:31:38", "commits": 1 }, { "source": "msmsTests-Vignette.Rnw", "filename": "msmsTests-Vignette.pdf", "title": "msmsTests: post test filters to improve reproducibility", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:31:38", "modified": "2013-11-01 20:31:38", "commits": 1 } ], "_score": 5.023663918197794, "_indexed": true, "_nocasepkg": "msmstests", "_universes": [ "bioc", "josepgregori" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.51.0", "date": "2026-05-30T10:07:11.000Z", "distro": "noble", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "a03e7b1416d2efe7255e0d46531ba5da3ef8a5eaaf90fdc1686b7bd2816dd0bc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.6.0", "os": "linux", "version": "1.51.0", "date": "2026-05-30T10:06:29.000Z", "distro": "noble", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "7d9a5592822047be1c1118b971471c9f9a040b987a36143710c5675ba5666d3f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-05-30T14:02:26.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "71af49729b63e51420fe838891699e1072c231c9d2e3120f5e05040284006d0c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.6.0", "os": "mac", "version": "1.51.0", "date": "2026-05-30T14:02:03.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "a4d4ff2a2628c1b9a1df32e040e2499c9cf0d21f7d493901ebb3b3a13970e26c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.6.0", "os": "wasm", "version": "1.51.0", "date": "2026-05-30T10:06:17.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "1e5af494a175027ec5a721a45ea27f6727643c285fb2ab80b8e943caaeefdefb", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.7.0", "os": "win", "version": "1.51.0", "date": "2026-05-30T10:05:00.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "460211378c62b6f4fd2117bda8eb0baaac2e99d5ee824b6ce1a3b49f5ab1a6d1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-05-30T10:04:52.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "7f628731f3291e2ff73895382a888fadddaaff96463a413c7dcd1b35533657a2", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" }, { "r": "4.6.0", "os": "win", "version": "1.51.0", "date": "2026-05-30T10:05:42.000Z", "commit": "36efb3a9419a448d69c5110a2990472703b43e6d", "fileid": "79a9ea4755b40fd9c44d31fb99b4c1469b087f81c5390a8e460792b17ce21baa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676421336" } ] }