{ "_id": "6a211ac8cd65a98ecbd1d39b", "Package": "SpectriPy", "Title": "Enhancing Cross-Language Mass Spectrometry Data Analysis with R\nand Python", "Version": "1.3.0", "Description": "The SpectriPy package allows integration of Python-based\nMS analysis code with the Spectra package. Spectra objects can\nbe converted into Python MS data structures. In addition,\nSpectriPy integrates and wraps the similarity scoring and\nprocessing/filtering functions from the Python matchms package\ninto R.", "Authors@R": "c(person(given = \"Michael\", family = \"Witting\",\nrole = c(\"aut\"),\nemail = \"michael.witting@helmholtz-muenchen.de\",\ncomment = c(ORCID = \"0000-0002-1462-4426\")),\nperson(given = \"Johannes\", family = \"Rainer\",\nemail = \"Johannes.Rainer@eurac.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6977-7147\")),\nperson(given = \"Carolin\", family = \"Huber\",\nemail = \"Carolin-elisabeth.huber@ufz.de\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-9355-8948\")),\nperson(given = \"Helge\", family = \"Hecht\",\nemail = \"helge.hecht@recetox.muni.cz\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-6744-996X\")),\nperson(given = \"Marilyn\", family = \"De Graeve\",\nemail = \"marilyn.degraeve@eurac.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-6916-401X\")),\nperson(given = \"Wout\", family = \"Bittremieux\",\nemail = \"wout.bittremieux@uantwerpen.be\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-3105-1359\")),\nperson(given = \"Thomas\", family = \"Naake\",\nemail = \"thomasnaake@googlemail.com\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-7917-5580\")),\nperson(given = \"Victor\", family = \"Chrone\",\nemail = \"vchrone@bmb.sdu.dk\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0007-2121-4066\")),\nperson(given = \"Matthias\", family = \"Anagho-Mattanovich\",\nemail = \"matthias.mattanovich@sund.ku.dk\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0001-7561-7898\")),\nperson(given = \"Pierre\", family = \"Marchal\",\nemail = \"pierre.marchal@unibe.ch\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0006-6567-6257\")),\nperson(given = \"Philippine\", family = \"Louail\",\nemail = \"philippine.louail@eurac.edu\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0009-0007-5429-6846\"))\n)", "License": "Artistic-2.0", "BugReports": "https://github.com/RforMassSpectrometry/SpectriPy/issues", "URL": "https://github.com/RforMassSpectrometry/SpectriPy", "biocViews": "Infrastructure, Metabolomics, MassSpectrometry, Proteomics", "Encoding": "UTF-8", "SystemRequirements": "python (>= 3.12), pandoc, quarto", "VignetteBuilder": "quarto", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Collate": "'conversion.R' 'MsBackendPython.R' 'compareSpectriPy.R'\n'filterSpectriPy.R' 'zzz.R'", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev python3", "Repository": "https://rformassspectrometry.r-universe.dev", "Date/Publication": "2026-05-12 06:37:37 UTC", "RemoteUrl": "https://github.com/rformassspectrometry/SpectriPy", "RemoteRef": "HEAD", "RemoteSha": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 13:50:21 UTC", "User": "root" }, "Author": "Michael Witting [aut] (ORCID: ),\nJohannes Rainer [aut, cre] (ORCID:\n),\nCarolin Huber [aut] (ORCID: ),\nHelge Hecht [ctb] (ORCID: ),\nMarilyn De Graeve [aut] (ORCID:\n),\nWout Bittremieux [aut] (ORCID: ),\nThomas Naake [aut] (ORCID: ),\nVictor Chrone [ctb] (ORCID: ),\nMatthias Anagho-Mattanovich [ctb] (ORCID:\n),\nPierre Marchal [ctb] (ORCID: ),\nPhilippine Louail [ctb] (ORCID:\n)", "Maintainer": "Johannes Rainer ", "MD5sum": "720ac89f7faad1f58bcd102699ed5cca", "_user": "rformassspectrometry", "_type": "src", "_file": "SpectriPy_1.3.0.tar.gz", "_fileid": "bdd2a62f4d5575effc2344ed4ba454fd0a32000f4fd48f6596a6fe810fe559d6", "_filesize": 1239567, "_sha256": "bdd2a62f4d5575effc2344ed4ba454fd0a32000f4fd48f6596a6fe810fe559d6", "_created": "2026-06-03T13:50:21.000Z", "_published": "2026-06-04T06:27:20.593Z", "_distro": "noble", "_jobs": [ { "job": 79461712514, "time": 509, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7386737376" }, { "job": 79461712654, "time": 500, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7386733994" }, { "job": 79461712116, "time": 204, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 79461712101, "time": 150, "config": "macos-release-arm64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79461712601, "time": 385, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7386509217" }, { "job": 79461712661, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7386579161" }, { "job": 79461712507, "time": 774, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7386852719" }, { "job": 79461712655, "time": 882, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7386899458" }, { "job": 79461712735, "time": 841, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7386881935" } ], "_buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/rformassspectrometry/SpectriPy", "_commit": { "id": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "author": "jorainer ", "committer": "jorainer ", "message": "ci: update R/BioC versions\n", "time": 1778567857 }, "_maintainer": { "name": "Johannes Rainer", "email": "johannes.rainer@eurac.edu", "login": "jorainer", "mastodon": "@jorainer@fediscience.org", "bluesky": "@jorainer.bsky.social", "linkedin": "in/jorainer", "orcid": "0000-0002-6977-7147", "description": "Computational Mass Spectrometry and Metabolomics, mostly; love R coding and Emacs; member of the Bioconductor Community Advisory Board.", "uuid": 5506112 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "reticulate", "version": ">= 1.42.0", "role": "Depends" }, { "package": "Spectra", "version": ">= 1.19.9", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "MsCoreUtils", "role": "Imports" }, { "package": "ProtGenerics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "snakecase", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "MsBackendMgf", "role": "Suggests" }, { "package": "MsDataHub", "role": "Suggests" }, { "package": "mzR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "rformassspectrometry", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-24", "n": 9 }, { "week": "2025-28", "n": 1 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-42", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2025-48", "n": 2 }, { "week": "2026-10", "n": 3 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 3 }, { "week": "2026-20", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.1", "bioc": "3.23" } ], "_topics": [ "infrastructure", "metabolomics", "massspectrometry", "proteomics", "mass-spectrometry", "python", "quarto" ], "_stars": 13, "_contributors": [ { "user": "jorainer", "count": 274, "uuid": 5506112 }, { "user": "mdgrv", "count": 46, "uuid": 82524629 }, { "user": "bittremieux", "count": 19, "uuid": 10773123 }, { "user": "tnaake", "count": 7, "uuid": 7208089 }, { "user": "michaelwitting", "count": 6, "uuid": 2734706 }, { "user": "guldchrone", "count": 5, "uuid": 90307023 }, { "user": "mmattano", "count": 5, "uuid": 57752712 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "hechth", "count": 4, "uuid": 12066490 }, { "user": "danielskatz", "count": 2, "uuid": 2913845 }, { "user": "lgatto", "count": 2, "uuid": 384198 }, { "user": "nilshoffmann", "count": 2, "uuid": 3309580 }, { "user": "chufz", "count": 1, "uuid": 38219063 }, { "user": "pimarchal", "count": 1, "uuid": 166733270 } ], "_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/SpectriPy" }, "_devurl": "https://github.com/rformassspectrometry/spectripy", "_searchresults": 28, "_quarto": true, "_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/readme.html", "extra/readme.md", "extra/SpectriPy.html", "manual.pdf" ], "_homeurl": "https://github.com/rformassspectrometry/spectripy", "_realowner": "bioc", "_cranurl": true, "_exports": [ "compareSpectriPy", "CosineGreedy", "CosineHungarian", "defaultSpectraVariableMapping", "filterSpectriPy", "ModifiedCosine", "ModifiedCosineGreedy", "ModifiedCosineHungarian", "MsBackendPy", "NeutralLossesCosine", "normalize_intensities", "pyspec_copy_on_replace", "pyspec_to_rspec", "reindex", "remove_peaks_around_precursor_mz", "rspec_to_pyspec", "select_by_intensity", "select_by_mz", "setBackend", "setSpectraVariableMapping", "spectraData<-", "spectraNames<-", "spectraVariableMapping", "spectraVariableMapping<-" ], "_help": [ { "page": "compareSpectriPy", "title": "Spectra similarity calculations using Python's matchms library", "topics": [ "compareSpectriPy", "compareSpectriPy,Spectra,missing,CosineGreedy-method", "compareSpectriPy,Spectra,Spectra,CosineGreedy-method", "CosineGreedy", "CosineHungarian", "ModifiedCosine", "ModifiedCosineGreedy", "ModifiedCosineHungarian", "NeutralLossesCosine" ] }, { "page": "conversion", "title": "Converting between R and Python MS data structures", "topics": [ "conversion", "defaultSpectraVariableMapping", "pyspec_to_rspec", "rspec_to_pyspec", "r_to_py.Spectra", "setSpectraVariableMapping", "spectraVariableMapping,character-method", "spectraVariableMapping,missing-method" ] }, { "page": "filterSpectriPy", "title": "Filter Spectra using Python's matchms library", "topics": [ "filterSpectriPy", "filterSpectriPy,Spectra,filter_param-method", "normalize_intensities", "remove_peaks_around_precursor_mz", "select_by_intensity", "select_by_mz" ] }, { "page": "MsBackendPy", "title": "A MS data backend for MS data stored in Python", "topics": [ "$,MsBackendPy-method", "$<-,MsBackendPy-method", "backendInitialize,MsBackendPy-method", "intensity<-,MsBackendPy-method", "length,MsBackendPy-method", "MsBackendPy", "mz<-,MsBackendPy-method", "peaksData,MsBackendPy-method", "peaksData<-,MsBackendPy-method", "reindex", "setBackend,Spectra,MsBackendPy-method", "spectraData,MsBackendPy-method", "spectraData<-,MsBackendPy-method", "spectraNames<-,MsBackendPy-method", "spectraVariableMapping,MsBackendPy-method", "spectraVariableMapping<-,MsBackendPy-method", "spectraVariables,MsBackendPy-method" ] }, { "page": "pyspec_copy_on_replace", "title": "Copy Python MS data structure on MS data replacement operations", "topics": [ "pyspec_copy_on_replace" ] } ], "_pkglogo": "https://github.com/rformassspectrometry/SpectriPy/raw/HEAD/logo.png", "_readme": "https://github.com/rformassspectrometry/SpectriPy/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocGenerics", "BiocParallel", "cli", "clue", "cluster", "codetools", "cpp11", "data.table", "formatR", "fs", "futile.logger", "futile.options", "generics", "glue", "here", "IRanges", "jsonlite", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MetaboCoreUtils", "MsCoreUtils", "png", "ProtGenerics", "rappdirs", "Rcpp", "RcppTOML", "reticulate", "rlang", "rprojroot", "S4Vectors", "snakecase", "snow", "Spectra", "stringi", "stringr", "vctrs", "withr" ], "_vignettes": [ { "source": "detailed-installation-configuration.qmd", "filename": "detailed-installation-configuration.html", "title": "Detailed information on installation and configuration", "engine": "quarto::html", "headings": [], "created": "2025-02-25 13:20:38", "modified": "2025-10-13 05:59:32", "commits": 7 }, { "source": "SpectriPy.qmd", "filename": "SpectriPy.html", "title": "Enabling integration of Python libraries and R packages for combined mass spectrometry data analysis", "engine": "quarto::html", "headings": [], "created": "2025-02-25 13:20:38", "modified": "2026-04-21 05:21:10", "commits": 15 } ], "_score": 7.8211727716341315, "_indexed": false, "_nocasepkg": "spectripy", "_universes": [ "rformassspectrometry" ], "_indexurl": "https://bioc.r-universe.dev/SpectriPy", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-06-03T13:53:58.000Z", "distro": "noble", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "de293937652a2fe21c79a6e061dafa3e088515b8a0584764b8e0d459f948be53", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-06-03T13:53:50.000Z", "distro": "noble", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "f5b4c843146e8281eb42ca93f716b2e6dc5e215773f93d95aeb1b8024fa9f8f3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-06-03T13:53:47.000Z", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "7a0dc8d0d098254ddedac84e27ef7f5e511d30e0ebb4c5802d8c789e5637cbdd", "status": "success", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-06-03T13:53:13.000Z", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "f3fdf553edb1bcd1211f5e1af5753cf9d664cafd5131f3ac9bafb0d17830c0fc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-06-03T13:53:55.000Z", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "4e58393e6e79d43652496d0b5ac5c8b726d7d84e6813f2c9f583d91b5be75011", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-06-03T13:53:42.000Z", "commit": "c0d1f7f6f0bfab6f9ee09490b5fd41f0e17dd089", "fileid": "13ffbb619f2f9a83538c0d40150439a66045acc770ed38c00bb382e5438af7a1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/rformassspectrometry/actions/runs/26888832075" } ] }