{ "_id": "6ab0f64e3d719c1f840851b1", "Package": "maldipickr", "Title": "Dereplicate and Cherry-Pick Mass Spectrometry Spectra", "Version": "1.3.3", "Authors@R": "c(\nperson(\"Charlie\", \"Pauvert\", , \"cpauvert@ukaachen.de\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-9832-2507\")),\nperson(\"David\", \"Wylensek\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8424-5712\")),\nperson(\"Selina\", \"Nüchtern\", role = \"ctb\"),\nperson(\"Thomas\", \"Clavel\", role = c(\"ctb\", \"fnd\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-7229-5595\"))\n)", "Description": "Convenient wrapper functions for the analysis of\nmatrix-assisted laser desorption/ionization-time-of-flight\n(MALDI-TOF) spectra data in order to select only representative\nspectra (also called cherry-pick). The package covers the\npreprocessing and dereplication steps (based on Strejcek,\nSmrhova, Junkova and Uhlik (2018)\n) needed to cluster MALDI-TOF\nspectra before the final cherry-picking step. It enables the\neasy exclusion of spectra and/or clusters to accommodate\ncomplex cherry-picking strategies. Alternatively,\ncherry-picking using taxonomic identification MALDI-TOF data is\nmade easy with functions to import inconsistently formatted\nreports.", "License": "GPL (>= 3)", "URL": "https://github.com/ClavelLab/maldipickr,\nhttps://clavellab.github.io/maldipickr/", "BugReports": "https://github.com/ClavelLab/maldipickr/issues", "VignetteBuilder": "knitr", "Config/fusen/version": "0.5.2", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Repository": "https://clavellab.r-universe.dev", "Date/Publication": "2026-06-23 11:04:34 UTC", "RemoteUrl": "https://github.com/clavellab/maldipickr", "RemoteRef": "HEAD", "RemoteSha": "0560a8f8255e963e415ff57608ae2b2637268191", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-21 09:13:49 UTC", "User": "root" }, "Author": "Charlie Pauvert [aut, cre, cph] (ORCID:\n),\nDavid Wylensek [ctb] (ORCID: ),\nSelina Nüchtern [ctb],\nThomas Clavel [ctb, fnd, cph] (ORCID:\n)", "Maintainer": "Charlie Pauvert ", "_user": "clavellab", "_type": "src", "_file": "maldipickr_1.3.3.tar.gz", "_fileid": "https://r2.ropensci.org/49cc55407dc6abb98b3af5c80fb5ad914eda19049ae6dd1679e8394c7949ff33", "_filesize": 2467748, "_sha256": "49cc55407dc6abb98b3af5c80fb5ad914eda19049ae6dd1679e8394c7949ff33", "_expires": "2026-12-30T09:18:04.000Z", "_created": "2026-09-21T09:13:49.000Z", "_published": "2026-09-21T09:18:06.611Z", "_jobs": [ { "job": 106277142047, "time": 142, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10630985410" }, { "job": 106277142081, "time": 130, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10630134535" }, { "job": 106277142063, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10631095319" }, { "job": 106277142211, "time": 202, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10631025410" }, { "job": 106276090122, "time": 216, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10630930183" }, { "job": 106277142049, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10630608320" }, { "job": 106277142202, "time": 91, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10630990323" }, { "job": 106277142126, "time": 85, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10630458896" }, { "job": 106277142148, "time": 96, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10630633205" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284", "_status": "success", "_upstream": "https://github.com/clavellab/maldipickr", "_commit": { "id": "0560a8f8255e963e415ff57608ae2b2637268191", "author": "cpauvert ", "committer": "cpauvert ", "message": "fix link to release v1.3.3\n", "time": 1782212674 }, "_maintainer": { "name": "Charlie Pauvert", "email": "cpauvert@ukaachen.de", "login": "cpauvert", "orcid": "0000-0001-9832-2507", "description": "", "uuid": 12406679 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "MALDIquant", "role": "Imports" }, { "package": "readBrukerFlexData", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "coop", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "clavellab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-08", "n": 1 }, { "week": "2026-21", "n": 1 }, { "week": "2026-26", "n": 8 } ], "_tags": [ { "name": "v1.3.3", "date": "2026-06-23" } ], "_topics": [ "cherry-pick", "dereplication", "maldi-tof-ms" ], "_stars": 3, "_contributors": [ { "user": "cpauvert", "count": 283, "uuid": 12406679 } ], "_userbio": { "uuid": 99190958, "type": "organization", "name": "The Clavel lab", "followers": 7, "description": "This is the official GitHub account for the research group of Prof. Thomas Clavel." }, "_downloads": { "count": 433, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/maldipickr" }, "_devurl": "https://github.com/clavellab/maldipickr", "_pkgdown": "https://clavellab.github.io/maldipickr/", "_searchresults": 11, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/maldipickr.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/clavellab/maldipickr", "_realowner": "clavellab", "_cranurl": true, "_releases": [ { "version": "1.1.1", "date": "2023-09-07" }, { "version": "1.2.0", "date": "2023-10-25" }, { "version": "1.3.0", "date": "2023-12-14" }, { "version": "1.3.1", "date": "2024-09-12" }, { "version": "1.3.3", "date": "2026-06-23" } ], "_exports": [ "%>%", "check_spectra", "delineate_with_identification", "delineate_with_similarity", "gather_spectra_stats", "get_spectra_names", "import_biotyper_spectra", "import_spede_clusters", "is_well_on_edge", "merge_processed_spectra", "pick_spectra", "process_spectra", "read_biotyper_report", "read_many_biotyper_reports", "remove_spectra", "set_reference_spectra" ], "_help": [ { "page": "check_spectra", "title": "Evaluate the spectra regularities", "topics": [ "check_spectra" ] }, { "page": "delineate_with_identification", "title": "Delineate clusters from taxonomic identifications", "topics": [ "delineate_with_identification" ] }, { "page": "delineate_with_similarity", "title": "Delineate clusters from a similarity matrix", "topics": [ "delineate_with_similarity" ] }, { "page": "gather_spectra_stats", "title": "Aggregate spectra quality-check statistics", "topics": [ "gather_spectra_stats" ] }, { "page": "get_spectra_names", "title": "Extract spectra names and check for uniqueness", "topics": [ "get_spectra_names" ] }, { "page": "import_biotyper_spectra", "title": "Importing spectra from the Bruker MALDI Biotyper device", "topics": [ "import_biotyper_spectra" ] }, { "page": "import_spede_clusters", "title": "Import clusters results generated by SPeDE", "topics": [ "import_spede_clusters" ] }, { "page": "is_well_on_edge", "title": "Identify the wells on the plate's edge", "topics": [ "is_well_on_edge" ] }, { "page": "merge_processed_spectra", "title": "Merge multiple processed spectra and peaks", "topics": [ "merge_processed_spectra" ] }, { "page": "pick_spectra", "title": "Cherry-pick Bruker MALDI Biotyper spectra", "topics": [ "pick_spectra" ] }, { "page": "process_spectra", "title": "Process Bruker MALDI Biotyper spectra _à la_ Strejcek et al. (2018)", "topics": [ "process_spectra" ] }, { "page": "read_biotyper_report", "title": "Importing Bruker MALDI Biotyper CSV report", "topics": [ "read_biotyper_report" ] }, { "page": "read_many_biotyper_reports", "title": "Importing a list of Bruker MALDI Biotyper CSV reports", "topics": [ "read_many_biotyper_reports" ] }, { "page": "remove_spectra", "title": "Remove (raw or processed) spectra", "topics": [ "remove_spectra" ] }, { "page": "set_reference_spectra", "title": "Set a reference spectrum for each cluster", "topics": [ "set_reference_spectra" ] } ], "_pkglogo": "https://repository-images.githubusercontent.com/613291736/be5379b5-ce72-430d-bb4c-70155ba6a0ad", "_readme": "https://github.com/clavellab/maldipickr/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "dplyr", "generics", "glue", "lifecycle", "magrittr", "MALDIquant", "pillar", "pkgconfig", "purrr", "R6", "readBrukerFlexData", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "dereplicate-bruker-maldi-biotyper-spectra.Rmd", "filename": "dereplicate-bruker-maldi-biotyper-spectra.html", "title": "Dereplicate Bruker MALDI Biotyper spectra", "engine": "knitr::rmarkdown", "headings": [ "Process Bruker MALDI Biotyper spectra", "Process from raw spectra to peak filtering", "Merge multiple processed spectra", "Compute a similarity matrix between all processed spectra (not included)", "Delineate clusters of spectra", "From a similarity matrix", "Similarity to clusters", "Set a reference spectrum for each cluster", "From taxonomic identifications", "Import clusters results generated by SPeDE", "Cherry-pick Bruker MALDI Biotyper spectra", "References" ], "created": "2023-03-23 13:05:21", "modified": "2024-05-06 10:51:07", "commits": 19 }, { "source": "import-data-from-bruker-maldi-biotyper.Rmd", "filename": "import-data-from-bruker-maldi-biotyper.html", "title": "Import data from Bruker MALDI Biotyper", "engine": "knitr::rmarkdown", "headings": [ "Importing generated reports from the Bruker MALDI Biotyper device", "Importing a single report", "Importing multiple reports", "Importing spectra from the Bruker MALDI Biotyper device", "Importing multiple spectra from a directory hierarchy", "Evaluate the quality of the spectra" ], "created": "2023-03-10 16:25:13", "modified": "2023-09-05 12:08:40", "commits": 9 }, { "source": "maldipickr.Rmd", "filename": "maldipickr.html", "title": "maldipickr", "engine": "knitr::rmarkdown", "headings": [ "Quickstart", "Using taxonomic identification report", "Get example data", "Delineate clusters and cherry-pick", "Using spectra data", "Session information" ], "created": "2024-09-11 14:50:02", "modified": "2024-09-11 15:27:24", "commits": 2 } ], "_score": 5.171726453653231, "_indexed": true, "_nocasepkg": "maldipickr", "_universes": [ "clavellab", "cpauvert" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.3", "date": "2026-09-21T09:16:06.000Z", "distro": "resolute", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/4c1e0dc002773a0a0aa2b255d8fcacbe98370bdfd3032cd20138b2294b8405c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.6.1", "os": "linux", "version": "1.3.3", "date": "2026-09-21T09:16:00.000Z", "distro": "resolute", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/d2302ade4d2435029ad397034f1602143994a942f51d422c99f14406ce7774c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.5.3", "os": "mac", "version": "1.3.3", "date": "2026-09-21T09:16:38.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/d9112e47f681259dddcf7505b8a218018bbf5000c3ff856074b50c37dd93bbdb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.6.1", "os": "mac", "version": "1.3.3", "date": "2026-09-21T09:16:24.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/f07775b7cacba6b754c070660da56520b9b37f92bd85fcb3b10e13e0131e5da0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.3", "date": "2026-09-21T09:16:20.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/9ec928fd63f2c5b296b4de22a0e3f4d529556a66a9ede5b105568911a3fd8229", "status": "success", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.7.0", "os": "win", "version": "1.3.3", "date": "2026-09-21T09:15:04.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/79fbbf0b8cd0cf5c67efb1602e1700eb364f55e6c8f37871befea4d8785cb310", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.5.3", "os": "win", "version": "1.3.3", "date": "2026-09-21T09:15:05.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/c557f643a03094d675f47c85922af9a4822e331cac1cf31a76f73b33e8fd4f20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" }, { "r": "4.6.1", "os": "win", "version": "1.3.3", "date": "2026-09-21T09:15:10.000Z", "commit": "0560a8f8255e963e415ff57608ae2b2637268191", "fileid": "https://r2.ropensci.org/b66a65b93ce7026c78b730b63afb461e8efbb70b86f78b52294d0fcdd2943f0a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/clavellab/actions/runs/35581752284" } ] }