{ "_id": "6a203338cd65a98ecbd10989", "Package": "PSMatch", "Title": "Handling and Managing Peptide Spectrum Matches", "Version": "1.17.1", "Authors@R": "c(person(given = \"Laurent\", family = \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-1520-2268\")),\nperson(given = \"Johannes\", family = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Sebastian\", family = \"Gibb\",\nemail = \"mail@sebastiangibb.de\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-7406-4443\")),\nperson(given = \"Samuel\", family = \"Wieczorek\",\nemail = \"samuel.wieczorek@cea.fr\",\nrole = \"ctb\"),\nperson(given = \"Thomas\", family = \"Burger\",\nemail = \"thomas.burger@cea.fr\",\nrole = \"ctb\"),\nperson(given = \"Guillaume\", family = \"Deflandre\",\nemail = \"guillaume.deflandre@uclouvain.be\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0009-0008-1257-2416\")))", "Description": "The PSMatch package helps proteomics practitioners to\nload, handle and manage Peptide Spectrum Matches. It provides\nfunctions to model peptide-protein relations as adjacency\nmatrices and connected components, visualise these as graphs\nand make informed decision about shared peptide filtering. The\npackage also provides functions to calculate and visualise MS2\nfragment ions.", "License": "Artistic-2.0", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "BugReports": "https://github.com/RforMassSpectrometry/PSM/issues", "URL": "https://github.com/RforMassSpectrometry/PSM", "biocViews": "Infrastructure, Proteomics, MassSpectrometry", "Config/roxygen2/version": "8.0.0", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://rformassspectrometry.r-universe.dev", "Date/Publication": "2026-05-20 15:56:30 UTC", "RemoteUrl": "https://github.com/rformassspectrometry/psmatch", "RemoteRef": "HEAD", "RemoteSha": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 13:50:26 UTC", "User": "root" }, "Author": "Laurent Gatto [aut, cre] (ORCID:\n),\nJohannes Rainer [aut] (ORCID: ),\nSebastian Gibb [aut] (ORCID: ),\nSamuel Wieczorek [ctb],\nThomas Burger [ctb],\nGuillaume Deflandre [ctb] (ORCID:\n)", "Maintainer": "Laurent Gatto ", "MD5sum": "51a17a6b60ae5a10a55b5863ba14ebf6", "_user": "rformassspectrometry", "_type": "src", "_file": "PSMatch_1.17.1.tar.gz", "_fileid": "5da6c73074e483d98ef91e10a0299c8deeff084bb742db16cd4beb38c3e39dea", "_filesize": 1159266, "_sha256": "5da6c73074e483d98ef91e10a0299c8deeff084bb742db16cd4beb38c3e39dea", "_created": "2026-06-03T13:50:26.000Z", "_published": "2026-06-03T13:59:19.993Z", "_distro": "noble", "_jobs": [ { "job": 79310213421, "time": 378, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7386678867" }, { "job": 79310213141, "time": 436, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7386704856" }, { "job": 79310213206, "time": 341, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7386661478" }, { "job": 79310212952, "time": 266, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7386628582" }, { "job": 79308728716, "time": 414, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7386507640" }, { "job": 79310213033, "time": 189, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7386593987" }, { "job": 79310212994, "time": 355, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7386668697" }, { "job": 79310213154, "time": 391, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7386684607" }, { "job": 79310212919, "time": 323, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7386654851" } ], "_buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rformassspectrometry/psmatch", "_commit": { "id": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "author": "Laurent Gatto ", "committer": "GitHub ", "message": "Merge pull request #44 from guideflandre/plotSpectraPTM\n\nAdd default charge up to precursor charge in plotSpectraPTM", "time": 1779292590 }, "_maintainer": { "name": "Laurent Gatto", "email": "laurent.gatto@uclouvain.be", "login": "lgatto", "mastodon": "@lgatto@fediscience.org", "orcid": "0000-0002-1520-2268", "description": "Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.\n", "uuid": 384198 }, "_registered": true, "_dependencies": [ { "package": "S4Vectors", "role": "Depends" }, { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "PTMods", "version": ">= 0.99.4", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Spectra", "version": ">= 1.17.10", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "ProtGenerics", "version": ">= 1.27.1", "role": "Imports" }, { "package": "QFeatures", "role": "Imports" }, { "package": "MsCoreUtils", "role": "Imports" }, { "package": "MsDataHub", "role": "Suggests" }, { "package": "rpx", "role": "Suggests" }, { "package": "mzID", "role": "Suggests" }, { "package": "mzR", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "factoextra", "role": "Suggests" }, { "package": "vdiffr", "version": ">= 1.0.0", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "rformassspectrometry", "_selfowned": true, "_usedby": 40, "_updates": [ { "week": "2025-23", "n": 3 }, { "week": "2025-25", "n": 3 }, { "week": "2025-28", "n": 3 }, { "week": "2025-31", "n": 3 }, { "week": "2025-51", "n": 6 }, { "week": "2026-12", "n": 1 }, { "week": "2026-14", "n": 4 }, { "week": "2026-15", "n": 4 }, { "week": "2026-21", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.17.0", "bioc": "3.24" }, { "branch": "release", "version": "1.16.0", "bioc": "3.23" } ], "_topics": [ "infrastructure", "proteomics", "massspectrometry", "mass-spectrometry", "peptide-spectrum-matches" ], "_stars": 6, "_contributors": [ { "user": "lgatto", "count": 299, "uuid": 384198 }, { "user": "guideflandre", "count": 199, "uuid": 37773040 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "sgibb", "count": 4, "uuid": 1828443 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 51361942, "type": "organization", "name": "RforMassSpectrometry", "description": "R packages for mass spectrometry" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PSMatch" }, "_devurl": "https://github.com/rformassspectrometry/psm", "_searchresults": 34, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PSMatch.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rformassspectrometry/psmatch", "_realowner": "bioc", "_cranurl": true, "_exports": [ "adjacencyMatrix", "calculateFragments", "ccMatrix", "connectedComponents", "ConnectedComponents", "defaultNeutralLoss", "describePeptides", "describeProteins", "dims", "filterPsmDecoy", "filterPsmFdr", "filterPsmRank", "filterPSMs", "filterPsmShared", "getAminoAcids", "getAtomicMass", "labelFragments", "makeAdjacencyMatrix", "makePeptideProteinVector", "ncols", "nrows", "plotAdjacencyMatrix", "plotSpectraPTM", "prioritiseConnectedComponents", "prioritizeConnectedComponents", "PSM", "psmVariables", "readPSMs", "reduced", "reduced<-", "reducePSMs" ], "_help": [ { "page": "adjacencyMatrix", "title": "Convert to/from an adjacency matrix.", "topics": [ "adjacencyMatrix", "makeAdjacencyMatrix", "makePeptideProteinVector", "plotAdjacencyMatrix" ] }, { "page": "calculateFragments", "title": "Calculate ions produced by fragmentation with variable modifications", "topics": [ "calculateFragments", "calculateFragments,character,missing-method", "defaultNeutralLoss", "modificationPositions" ] }, { "page": "ConnectedComponents", "title": "Connected components", "topics": [ "adjacencyMatrix,ConnectedComponents", "adjacencyMatrix,ConnectedComponents-method", "ccMatrix", "ConnectedComponents", "connectedComponents", "ConnectedComponents-class", "dims,ConnectedComponents", "dims,ConnectedComponents-method", "length,ConnectedComponents", "length,ConnectedComponents-method", "ncols,ConnectedComponents", "ncols,ConnectedComponents-method", "nrows,ConnectedComponents", "nrows,ConnectedComponents-method", "prioritiseConnectedComponents", "prioritizeConnectedComponents", "show,ConnectedComponents", "[,ConnectedComponents,integer,ANY,ANY", "[,ConnectedComponents,integer,ANY,ANY-method", "[,ConnectedComponents,logical,ANY,ANY", "[,ConnectedComponents,logical,ANY,ANY-method", "[,ConnectedComponents,numeric,ANY,ANY", "[,ConnectedComponents,numeric,ANY,ANY-method" ] }, { "page": "describeProteins", "title": "Describe protein and peptide compositions", "topics": [ "describePeptides", "describeProteins" ] }, { "page": "filterPSMs", "title": "Filter out unreliable PSMs.", "topics": [ "filterPsmDecoy", "filterPsmFdr", "filterPsmRank", "filterPSMs", "filterPsmShared" ] }, { "page": "getAminoAcids", "title": "Amino acids", "topics": [ "getAminoAcids" ] }, { "page": "getAtomicMass", "title": "Atomic mass.", "topics": [ "getAtomicMass" ] }, { "page": "labelFragments", "title": "labels MS2 Fragments", "topics": [ "labelFragments" ] }, { "page": "plotSpectraPTM", "title": "Function to plot MS/MS spectra with PTMs", "topics": [ "plotSpectraPTM" ] }, { "page": "PSM", "title": "A class for peptide-spectrum matches", "topics": [ "adjacencyMatrix,PSM-method", "PSM", "PSM,character", "PSM,data.frame", "PSM,PSM", "PSM-class", "psmVariables", "readPSMs", "reduced", "reduced<-", "reducePSMs" ] }, { "page": "PSMatch", "title": "PSMatch: Handling and Managing Peptide Spectrum Matches", "topics": [ "PSMatch-package", "PSMatch" ] } ], "_readme": "https://github.com/rformassspectrometry/psmatch/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocParallel", "bslib", "cachem", "cli", "clue", "cluster", "codetools", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "IRanges", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "MultiAssayExperiment", "openssl", "otel", "pillar", "pkgconfig", "plotly", "plyr", "promises", "ProtGenerics", "PTMods", "purrr", "QFeatures", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "Spectra", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "Fragments.Rmd", "filename": "Fragments.html", "title": "MS2 fragment ions", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Calculating fragment ions", "Visualising fragment ions", "Customising charge states", "Session information" ], "created": "2022-02-14 12:01:25", "modified": "2026-05-20 15:56:30", "commits": 8 }, { "source": "AdjacencyMatrix.Rmd", "filename": "AdjacencyMatrix.html", "title": "Understanding protein groups with adjacency matrices", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Peptide-protein relation", "Visualising adjacency matrices", "Colouring the graph nodes", "Colouring protein nodes", "Colouring peptide nodes", "Using quantitative data", "Prioritising connected components", "Session information" ], "created": "2022-02-09 09:07:54", "modified": "2026-04-03 21:21:14", "commits": 12 }, { "source": "PSM.Rmd", "filename": "PSM.html", "title": "Working with PSM data", "engine": "knitr::rmarkdown", "headings": [ "Installation instructions", "Introduction", "Handling and processing identification data", "Loading PSM data", "Keeping all matches", "Filtering data", "Remove decoy hits", "Keep first rank matches", "Remove shared peptides", "All filters in one function", "The mzR and mzID parsers", "Session information" ], "created": "2020-10-28 21:57:03", "modified": "2026-04-05 06:10:22", "commits": 12 } ], "_score": 9.121205173296492, "_indexed": false, "_nocasepkg": "psmatch", "_universes": [ "rformassspectrometry" ], "_indexurl": "https://bioc.r-universe.dev/PSMatch", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.1", "date": "2026-06-03T13:53:51.000Z", "distro": "noble", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "b70274df6f123f67a759df896ad5a0c31f185275c0a9d6670527c9423ca8787f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.6.0", "os": "linux", "version": "1.17.1", "date": "2026-06-03T13:54:28.000Z", "distro": "noble", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "cd7787951deef27898666bc6831487e4626230605553b065f102d1e20606c049", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.5.3", "os": "mac", "version": "1.17.1", "date": "2026-06-03T13:52:47.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "b3d08188882e044348cfab5466f03cdf0dc35b2c68af4b168857250af2da3d18", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.6.0", "os": "mac", "version": "1.17.1", "date": "2026-06-03T13:52:39.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "227db4c3078e59e86eb23d540a7f4b63e1fc536b73f2e5ca213a0851f7393ecd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.1", "date": "2026-06-03T13:54:18.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "b9d4d1ba8626b234ff9285dde50e3f5585579c1e6713f26c0a8d7e469a0b8186", "status": "success", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.7.0", "os": "win", "version": "1.17.1", "date": "2026-06-03T13:53:02.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "3545c4d697f25a8f884405301d46dddb2d6c2cf6010f0524a69e18e1da7f2174", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.5.3", "os": "win", "version": "1.17.1", "date": "2026-06-03T13:52:40.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "e4ce0259b4a23dfe39b8f16669a6cde203413feac3ec6b7bf3a762e83ac7e7a9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" }, { "r": "4.6.0", "os": "win", "version": "1.17.1", "date": "2026-06-03T13:52:36.000Z", "commit": "ff1b83c66e28c7c6e93c55ee456ad92772ba2afb", "fileid": "89921bd358919fca73b800764c54b7fab2ff10b4b6089e60c8948b9bda92fd91", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888818308" } ] }