{ "_id": "6a1861e6acfb0bcc41dbe74a", "Package": "artMS", "Type": "Package", "Title": "Analytical R tools for Mass Spectrometry", "Version": "1.31.0", "Date": "2021-07-13", "Authors@R": "c(person(\"David\", \"Jimenez-Morales\", role = c(\"aut\",\"cre\"),\nemail = \"biodavidjm@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4356-6461\")),\nperson(\"Alexandre\", \"Rosa Campos\", role = c(\"aut\",\"ctb\"),\ncomment = c(ORCID = \"0000-0003-3988-7764\")),\nperson(\"John\", \"Von Dollen\", role = c(\"aut\")),\nperson(\"Nevan\", \"Krogan\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4902-337X\")),\nperson(\"Danielle\", \"Swaney\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0001-6119-6084\")))", "Description": "artMS provides a set of tools for the analysis of\nproteomics label-free datasets. It takes as input the MaxQuant\nsearch result output (evidence.txt file) and performs quality\ncontrol, relative quantification using MSstats, downstream\nanalysis and integration. artMS also provides a set of\nfunctions to re-format and make it compatible with other\nanalytical tools, including, SAINTq, SAINTexpress, Phosfate,\nand PHOTON. Check [http://artms.org](http://artms.org) for\ndetails.", "License": "GPL (>= 3) + file LICENSE", "URL": "http://artms.org", "BugReports": "https://github.com/biodavidjm/artMS/issues", "Encoding": "UTF-8", "LazyLoad": "yes", "LazyData": "true", "biocViews": "Proteomics, DifferentialExpression, BiomedicalInformatics,\nSystemsBiology, MassSpectrometry, Annotation, QualityControl,\nGeneSetEnrichment, Clustering, Normalization, ImmunoOncology,\nMultipleComparison", "NeedsCompilation": "no", "VignetteBuilder": "knitr", "RoxygenNote": "7.1.1", "Roxygen": "list(markdown = TRUE)", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:06 UTC", "RemoteUrl": "https://github.com/bioc/artMS", "RemoteRef": "HEAD", "RemoteSha": "4f07b3978e0cabc01fa8c6af07628d1874b45a63", "Packaged": { "Date": "2026-05-28 14:50:02 UTC", "User": "root" }, "Author": "David Jimenez-Morales [aut, cre] (ORCID:\n),\nAlexandre Rosa Campos [aut, ctb] (ORCID:\n),\nJohn Von Dollen [aut],\nNevan Krogan [aut] (ORCID: ),\nDanielle Swaney [aut, ctb] (ORCID:\n)", "Maintainer": "David Jimenez-Morales ", "MD5sum": "430b5b54be3b4827373162e15002d842", "_user": "bioc", "_type": "src", "_file": "artMS_1.31.0.tar.gz", "_fileid": "2f452342f803e9f88b03f1b44e6534a238d4bb093168543d24946a5b4117517b", "_filesize": 4010811, "_sha256": "2f452342f803e9f88b03f1b44e6534a238d4bb093168543d24946a5b4117517b", "_created": "2026-05-28T14:50:02.000Z", "_published": "2026-05-28T15:40:22.829Z", "_jobs": [ { "job": 78318456724, "time": 263, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7269244367" }, { "job": 78318456880, "time": 514, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7269351513" }, { "job": 78318456941, "time": 445, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7269322408" }, { "job": 78318456707, "time": 242, "config": 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dataset", "topics": [ "artms_data_ph_config" ] }, { "page": "artms_data_ph_contrast", "title": "Contrast example for the PH dataset", "topics": [ "artms_data_ph_contrast" ] }, { "page": "artms_data_ph_evidence", "title": "Evidence file example", "topics": [ "artms_data_ph_evidence" ] }, { "page": "artms_data_ph_keys", "title": "Keys File Example", "topics": [ "artms_data_ph_keys" ] }, { "page": "artms_data_ph_msstats_modelqc", "title": "MSstats modelQC example", "topics": [ "artms_data_ph_msstats_modelqc" ] }, { "page": "artms_data_ph_msstats_results", "title": "MSstats results example", "topics": [ "artms_data_ph_msstats_results" ] }, { "page": "artms_data_randomDF", "title": "Random data set", "topics": [ "artms_data_randomDF" ] }, { "page": "artmsAnalysisQuantifications", "title": "Analysis of the Relative Quantifications", "topics": [ "artmsAnalysisQuantifications" ] }, { "page": "artmsAnnotateSpecie", "title": "Adding a column with the species name", "topics": [ 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(summary.txt based)", "RELATIVE QUANTIFICATION", "Quantification of Changes in Global Protein Abundance", "Quantification of Changes in Global Phosphorylation, Ubiquitination, Acetylation (or any PTM)", "PTM-Site/Peptide-specific Quantification of Changes (PH, UB, AC)", "Output files", "TXT (tab delimited) files", "Plots (pdf)", "ANALYSIS OF QUANTIFICATIONS", "Inputs", "Outputs", "MISCELLANEOUS FUNCTIONS", "Annotate data.frame with Gene Symbol, Name, ENTREZ based on Uniprot IDs", "Average Intensity, RT, CR", "Change column name", "Individual abundance dot plots", "Enrichment analysis function", "Enrichment analysis using gProfileR", "MaxQuant evidence file to SAINTexpress format", "MaxQuant evidence file to SAINTq format", "Generate Phosfate input file", "Generate Photon input file", "Remove contaminants and empty proteins from the MaxQuant evidence file", "Generate ph-site specific evidence file", "METABOLOMICS", "Convert Metabolomics", "QC Metabolomics", "Relative Quantification:", "TESTING FILES", "HELP" ], "created": "2018-06-13 01:08:40", "modified": "2021-07-14 06:53:05", "commits": 59 } ], "_score": 6.702430536445525, "_indexed": true, "_nocasepkg": "artms", "_universes": [ "bioc", "biodavidjm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.31.0", "date": "2026-05-28T14:57:48.000Z", "distro": "noble", "commit": "4f07b3978e0cabc01fa8c6af07628d1874b45a63", "fileid": "1ff0d7a841ef468bb260ee3fac86677347216f4943a80a94becc222b0f26ee5a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581748040" }, { "r": "4.6.0", "os": "linux", "version": "1.31.0", "date": "2026-05-28T14:56:48.000Z", "distro": "noble", "commit": "4f07b3978e0cabc01fa8c6af07628d1874b45a63", "fileid": "0292b40bb5553d13a94bda4947b6beb762e3726aae5a6c8a33228f5b5eb03050", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26581748040" }, { "r": "4.5.3", "os": "mac", "version": "1.31.0", 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