{
  "_id": "6a1d286e1d7bb097a0a38483",
  "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://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:05:10 UTC",
  "RemoteUrl": "https://github.com/bioc/SpectriPy",
  "RemoteRef": "HEAD",
  "RemoteSha": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:36:26 UTC",
    "User": "root"
  },
  "Author": "Michael Witting [aut] (ORCID: <https://orcid.org/0000-0002-1462-4426>),\nJohannes Rainer [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6977-7147>),\nCarolin Huber [aut] (ORCID: <https://orcid.org/0000-0002-9355-8948>),\nHelge Hecht [ctb] (ORCID: <https://orcid.org/0000-0001-6744-996X>),\nMarilyn De Graeve [aut] (ORCID:\n<https://orcid.org/0000-0001-6916-401X>),\nWout Bittremieux [aut] (ORCID: <https://orcid.org/0000-0002-3105-1359>),\nThomas Naake [aut] (ORCID: <https://orcid.org/0000-0001-7917-5580>),\nVictor Chrone [ctb] (ORCID: <https://orcid.org/0009-0007-2121-4066>),\nMatthias Anagho-Mattanovich [ctb] (ORCID:\n<https://orcid.org/0000-0001-7561-7898>),\nPierre Marchal [ctb] (ORCID: <https://orcid.org/0009-0006-6567-6257>),\nPhilippine Louail [ctb] (ORCID:\n<https://orcid.org/0009-0007-5429-6846>)",
  "Maintainer": "Johannes Rainer <Johannes.Rainer@eurac.edu>",
  "MD5sum": "fba5ca9982bdf1d36b76069dfc415177",
  "_user": "bioc",
  "_type": "src",
  "_file": "SpectriPy_1.3.0.tar.gz",
  "_fileid": "208aec5423df70f214fb55abe699d7b54604190e66c2be69355d7ca6d09c89e1",
  "_filesize": 1241577,
  "_sha256": "208aec5423df70f214fb55abe699d7b54604190e66c2be69355d7ca6d09c89e1",
  "_created": "2026-05-30T09:36:26.000Z",
  "_published": "2026-06-01T06:36:30.658Z",
  "_jobs": [
    {
      "job": 78798378449,
      "time": 219,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307335409"
    },
    {
      "job": 78798378289,
      "time": 517,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307363455"
    },
    {
      "job": 78798378540,
      "time": 471,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307359282"
    },
    {
      "job": 78798377854,
      "time": 149,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798377839,
      "time": 143,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 78798377827,
      "time": 433,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307228801"
    },
    {
      "job": 78798378099,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307328264"
    },
    {
      "job": 78798378123,
      "time": 879,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7307393736"
    },
    {
      "job": 78798378279,
      "time": 739,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7307380966"
    },
    {
      "job": 78798378253,
      "time": 737,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7307380881"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/SpectriPy",
  "_commit": {
    "id": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381510
  },
  "_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
  },
  "_distro": "noble",
  "_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": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 1
    },
    {
      "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": 1
    },
    {
      "week": "2026-18",
      "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": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 172,
    "source": "https://www.bioconductor.org/packages/stats/bioc/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": false,
  "_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/bioc/SpectriPy/raw/HEAD/logo.png",
  "_readme": "https://github.com/bioc/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": 7.851135995011575,
  "_indexed": true,
  "_nocasepkg": "spectripy",
  "_universes": [
    "bioc",
    "jorainer",
    "rformassspectrometry"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-30T09:54:44.000Z",
      "distro": "noble",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "3c1f2a5d1b881749953b8c6796046820b499562c68187cb0d4bf912ec4e67ee6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.3.0",
      "date": "2026-05-30T09:54:26.000Z",
      "distro": "noble",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "baddd2a778bbce0e3282585fa451ae7179a4a2295317e9fb388a2c723314c158",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.3.0",
      "date": "2026-05-30T09:53:53.000Z",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "d5081bcdbab53619289a813eeef53fed31da385447bddcbe1009f25da28096e8",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:54:44.000Z",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "e5b7bf80db7d185c613060e436b1eed57ac5e3020ccd2eda9656776f5b073a8f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:52:34.000Z",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "0cb077b88b5b44e287139e6832a392e0bcf1a994e3de6f3272a1e240b0833eef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.3.0",
      "date": "2026-05-30T09:52:29.000Z",
      "commit": "c61370bce46b19ef871bb040e12bc2fc62a8027e",
      "fileid": "8c5de2e08b7f1051097140b0944af221fd9d33855269b399e2f408014a27ec43",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675727812"
    }
  ]
}