{ "_id": "6a1aedb91d7bb097a09f52cb", "Package": "msqrob2", "Title": "Robust statistical inference for quantitative LC-MS proteomics", "Version": "1.21.0", "Authors@R": "c(\nperson(given = \"Lieven\",\nfamily = \"Clement\",\nrole = c(\"aut\", \"cre\"),\nemail = \"lieven.clement@ugent.be\",\ncomment = c(ORCID = \"0000-0002-9050-4370\")),\nperson(given = \"Laurent\",\nfamily = \"Gatto\",\nrole = c(\"aut\"),\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\")),\nperson(family = \"Crook\",\ngiven = \"Oliver M.\",\nemail = \"oliver.crook@stats.ox.ac.uk\",\ncomment = c(ORCID = \"0000-0001-5669-8506\"),\nrole = \"aut\"),\nperson(given = \"Adriaan\",\nfamily = \"Sticker\",\nemail = \"adriaan.sticker@ugent.be\",\nrole = \"ctb\"),\nperson(given = \"Ludger\",\nfamily = \"Goeminne\",\nemail = \" ludgergoeminne@gmail.com\",\nrole = \"ctb\"),\nperson(given = \"Milan\",\nfamily = \"Malfait\",\nemail = \"milan.malfait94@gmail.com\",\ncomment = c(ORCID = \"0000-0001-9144-3701\"),\nrole = \"ctb\"),\nperson(given = \"Stijn\",\nfamily = \"Vandenbulcke\",\nemail = \"vandenbulcke.stijn@gmail.com\",\nrole = \"aut\")\n)", "Description": "msqrob2 provides a robust linear mixed model framework for\nassessing differential abundance in MS-based Quantitative\nproteomics experiments. Our workflows can start from raw\npeptide intensities or summarised protein expression values.\nThe model parameter estimates can be stabilized by ridge\nregression, empirical Bayes variance estimation and robust\nM-estimation. msqrob2's hurde workflow can handle missing data\nwithout having to rely on hard-to-verify imputation\nassumptions, and, outcompetes state-of-the-art methods with and\nwithout imputation for both high and low missingness. It builds\non QFeature infrastructure for quantitative mass spectrometry\ndata to store the model results together with the raw data and\npreprocessed data.", "License": "Artistic-2.0", "Collate": "'msqrob-framework.R' 'allGenerics.R' 'calculateNormFactors.R'\n'accessors.R' 'msqrob.R' 'msqrob-utils.R' 'StatModel-methods.R'\n'hypothesisTest-methods.R' 'msqrob-methods.R'\n'msqrobAggregate.R' 'topFeatures.R' 'data.R' 'msqrobQB.R'\n'msqrobHurdle-methods.R' 'collect-plot-results.R'", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Roxygen": "list(markdown=TRUE)", "RoxygenNote": "7.3.3", "biocViews": "Proteomics, Metabolomics, MassSpectrometry,\nDifferentialExpression, MultipleComparison, Regression,\nExperimentalDesign, Software, ImmunoOncology, Normalization,\nTimeCourse, Preprocessing", "URL": "https://github.com/statOmics/msqrob2", "BugReports": "https://github.com/statOmics/msqrob2/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:09 UTC", "RemoteUrl": "https://github.com/bioc/msqrob2", "RemoteRef": "HEAD", "RemoteSha": "af1cae40edbb8f54c4ee53028887b6693964cea8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:40:33 UTC", "User": "root" }, "Author": "Lieven Clement [aut, cre] (ORCID:\n),\nLaurent Gatto [aut] (ORCID: ),\nOliver M. Crook [aut] (ORCID: ),\nAdriaan Sticker [ctb],\nLudger Goeminne [ctb],\nMilan Malfait [ctb] (ORCID: ),\nStijn Vandenbulcke [aut]", "Maintainer": "Lieven Clement ", "MD5sum": "0709fce8de79b06ab8a20db735c17144", "_user": "bioc", "_type": "src", "_file": "msqrob2_1.21.0.tar.gz", "_fileid": "3813dfe9f1571c46a0f94d490f78187256c67a7cfd76bdfe6f4571f30fbc6554", "_filesize": 5347554, "_sha256": "3813dfe9f1571c46a0f94d490f78187256c67a7cfd76bdfe6f4571f30fbc6554", "_created": "2026-05-30T09:40:33.000Z", "_published": "2026-05-30T14:01:29.837Z", "_jobs": [ { "job": 78640307726, "time": 253, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307396451" }, { "job": 78640307739, "time": 470, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307415924" }, { "job": 78640307738, "time": 425, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307411917" }, { "job": 78640307732, "time": 219, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7308703428" }, { "job": 78640307727, "time": 247, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7308706250" }, { "job": 78639493972, "time": 475, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307253006" }, { "job": 78640307729, "time": 210, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307392503" }, { "job": 78640307743, "time": 385, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307407654" }, { "job": 78640307740, "time": 476, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307415827" }, { "job": 78640307736, "time": 424, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307411012" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675992935", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/msqrob2", "_commit": { "id": "af1cae40edbb8f54c4ee53028887b6693964cea8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380969 }, "_maintainer": { "name": "Lieven Clement", "email": "lieven.clement@ugent.be", "login": "lievenclement", "description": "I am Associate Professor of Statistical Genomics at Ghent University. 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