{ "_id": "6a1ac8451d7bb097a09dc0ae", "Package": "limpa", "Version": "1.5.0", "Date": "2026-04-26", "Title": "Quantification and Differential Analysis of Proteomics Data", "Description": "Quantification and differential analysis of\nmass-spectrometry proteomics data, with probabilistic recovery\nof information from missing values. Avoids the need for\nimputation. Estimates the detection probability curve (DPC),\nwhich relates the probability of successful detection to the\nunderlying log-intensity of each precursor ion, and uses it to\nincorporate missing values into protein quantification and into\nsubsequent differential expression analyses. The package\nproduces objects suitable for downstream analysis in limma. The\npackage accepts precursor (or peptide) intensities including\nmissing values and produces complete protein quantifications\nwithout the need for imputation. The uncertainty of the protein\nquantifications is propagated through to the limma analyses\nusing variance modeling and precision weights, ensuring\naccurate error rate control. The analysis pipeline can\nalternatively work with PTM or protein level data. The package\nname \"limpa\" is an acronym for \"Linear Models for Proteomics\nData\".", "Authors@R": "c(person(\"Mengbo\", \"Li\",\nemail = \"li.me@wehi.edu.au\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-9666-5810\")),\nperson(\"Pedro\", \"Baldoni\",\nemail = \"baldoni.p@wehi.edu.au\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-9510-8326\")),\nperson(\"Gordon\", \"Smyth\",\nemail = \"smyth@wehi.edu.au\",\nrole = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0001-9221-2892\")))", "License": "GPL (>=2)", "VignetteBuilder": "knitr", "URL": "https://github.com/SmythLab/limpa", "biocViews": "Bayesian, BiologicalQuestion, DataImport,\nDifferentialExpression, GeneExpression, MassSpectrometry,\nPreprocessing, Proteomics, Regression, Software", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:41 UTC", "RemoteUrl": "https://github.com/bioc/limpa", "RemoteRef": "HEAD", "RemoteSha": "8edf301af1aa41dd8ddcd75355ee925cc76d1383", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:48:56 UTC", "User": "root" }, "Author": "Mengbo Li [aut] (ORCID: ),\nPedro Baldoni [ctb] (ORCID: ),\nGordon Smyth [cre, aut] (ORCID:\n)", "Maintainer": "Gordon Smyth ", "MD5sum": "fb79c2993058bdff446a1debf90c8511", "_user": "bioc", "_type": "src", "_file": "limpa_1.5.0.tar.gz", "_fileid": "2b6767f73958f8356006ac317dfbd172e36e060d81fac2ab02d624afa9755a22", "_filesize": 568405, "_sha256": "2b6767f73958f8356006ac317dfbd172e36e060d81fac2ab02d624afa9755a22", "_created": "2026-05-30T07:48:56.000Z", "_published": "2026-05-30T11:21:41.479Z", "_jobs": [ { "job": 78634578733, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306612406" }, { "job": 78634578742, "time": 192, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306617029" }, { "job": 78634578740, "time": 218, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306619650" }, { "job": 78634578761, "time": 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