{ "_id": "6a572a03ff0138dec5d6e8ae", "Package": "RaMS", "Type": "Package", "Title": "R Access to Mass-Spec Data", "Version": "1.4.3", "Authors@R": "c(\nperson(given = \"William\", family = \"Kumler\", email = \"wkumler@uw.edu\",\nrole = c(\"aut\", \"cre\", \"cph\")),\nperson(given = \"Ricardo\", family = \"Cunha\", role = \"ctb\"),\nperson(given = \"Ethan\", family = \"Bass\", role = \"ctb\")\n)", "Maintainer": "William Kumler ", "Description": "R-based access to mass-spectrometry (MS) data. While many\npackages exist to process MS data, many of these make it\ndifficult to access the underlying mass-to-charge ratio (m/z),\nintensity, and retention time of the files themselves. This\npackage is designed to format MS data in a tidy fashion and\nallows the user perform the plotting and analysis.", "License": "MIT + file LICENSE", "URL": "https://github.com/wkumler/RaMS", "BugReports": "https://github.com/wkumler/RaMS/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libxml2-dev", "Repository": "https://wkumler.r-universe.dev", "Date/Publication": "2025-09-17 21:00:25 UTC", "RemoteUrl": "https://github.com/wkumler/rams", "RemoteRef": "HEAD", "RemoteSha": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-15 06:29:48 UTC", "User": "root" }, "Author": "William Kumler [aut, cre, cph],\nRicardo Cunha [ctb],\nEthan Bass [ctb]", "_user": "wkumler", "_type": "src", "_file": "RaMS_1.4.3.tar.gz", "_fileid": "https://r2.ropensci.org/d27eaf02a1f7f9638d5822c7ad90945a28bd30ddc7e1a426a837c545925a56b5", "_filesize": 3982824, "_sha256": "d27eaf02a1f7f9638d5822c7ad90945a28bd30ddc7e1a426a837c545925a56b5", "_expires": "2026-10-23T06:34:41.000Z", "_created": "2026-07-15T06:29:48.000Z", "_published": "2026-07-15T06:34:43.497Z", "_jobs": [ { "job": 87284467936, "time": 182, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8334538529" }, { "job": 87284467942, "time": 257, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8334561585" }, { "job": 87284467931, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8334539437" }, { "job": 87284467940, "time": 164, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8334523963" }, { "job": 87283806221, "time": 270, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8334483308" }, { "job": 87284467929, "time": 156, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8334530921" }, { "job": 87284467926, "time": 130, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8334523787" }, { "job": 87284467924, "time": 126, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8334522509" }, { "job": 87284467937, "time": 138, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8334526015" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080", "_status": "success", "_upstream": "https://github.com/wkumler/rams", "_commit": { "id": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "author": "wkumler ", "committer": "wkumler ", "message": "Revert \"Adding newline after progress bar to handle following text better\"\n\nThis reverts commit 7ae219287622d7f01ad775c396334138e9912311.\n", "time": 1758142825 }, "_maintainer": { "name": "William Kumler", "email": "wkumler@uw.edu", "login": "wkumler", "description": "Data science manager and recent chemical oceanography Ph.D. graduate at the University of Washington", "uuid": 43116923 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "xml2", "role": "Imports" }, { "package": "base64enc", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "openxlsx", "role": "Suggests" }, { "package": "DBI", "role": "Suggests" }, { "package": "RSQLite", "role": "Suggests" }, { "package": "reticulate", "role": "Suggests" }, { "package": "BiocParallel", "role": "Suggests" }, { "package": "Spectra", "role": "Suggests" }, { "package": "arrow", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "rvest", "role": "Suggests" } ], "_owner": "wkumler", "_selfowned": true, "_usedby": 8, "_updates": [ { "week": "2025-31", "n": 5 }, { "week": "2025-38", "n": 2 } ], "_tags": [], "_topics": [ "mass-spectrometry-data", "tidy-data" ], "_stars": 25, "_contributors": [ { "user": "wkumler", "count": 513, "uuid": 43116923 }, { "user": "ricardo-cunha", "count": 9, "uuid": 64540212 }, { "user": "ethanbass", "count": 4, "uuid": 15876283 } ], "_userbio": { "uuid": 43116923, "type": "user", "name": "William Kumler", "followers": 20, "description": "Data science manager and recent chemical oceanography Ph.D. graduate at the University of Washington" }, "_downloads": { "count": 656, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RaMS" }, "_mentions": 1, "_devurl": "https://github.com/wkumler/rams", "_searchresults": 131, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/RaMS.html", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/wkumler/rams", "_realowner": "wkumler", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-03-22" }, { "version": "1.3.0", "date": "2022-11-28" }, { "version": "1.3.1", "date": "2022-12-14" }, { "version": "1.3.4", "date": "2023-12-13" }, { "version": "1.4.0", "date": "2024-03-02" }, { "version": "1.4.3", "date": "2024-10-09" } ], "_exports": [ "%between%", "between", "editMSfileRTs", "grabAccessionData", "grabMSdata", "grabMzmlData", "grabMzxmlData", "minifyMSdata", "msdata_connection", "mz_group", "pmppm", "qplotMS1data", "tmzmlMaker", "trapz" ], "_help": [ { "page": "sub-.msdata_connection", "title": "S3 indexing for msdata_connection objects", "topics": [ "[.msdata_connection" ] }, { "page": "cash-.msdata_connection", "title": "S3 dollar sign notation for msdata_connection objects", "topics": [ "$.msdata_connection" ] }, { "page": "checkOutputQuality", "title": "Check that the output data is properly formatted.", "topics": [ "checkOutputQuality" ] }, { "page": "editMSfileRTs", "title": "Edit mzML/mzXML file retention times", "topics": [ "editMSfileRTs" ] }, { "page": "getEncoded", "title": "Convert from compressed binary to R numeric vector", "topics": [ "getEncoded" ] }, { "page": "giveEncoding", "title": "Convert from R numeric vector to compressed binary", "topics": [ "giveEncoding" ] }, { "page": "grabAccessionData", "title": "Get arbitrary metadata from an mzML file by accession number", "topics": [ "grabAccessionData" ] }, { "page": "grabMSdata", "title": "Grab mass-spectrometry data from file(s)", "topics": [ "grabMSdata" ] }, { "page": "grabMzmlBPC", "title": "Grab the BPC or TIC from a file", "topics": [ "grabMzmlBPC" ] }, { "page": "grabMzmlDAD", "title": "Extract the DAD data from an mzML nodeset", "topics": [ "grabMzmlDAD" ] }, { "page": "grabMzmlData", "title": "Get mass-spectrometry data from an mzML file", "topics": [ "grabMzmlData" ] }, { "page": "grabMzmlEncodingData", "title": "Helper function to extract mzML file encoding data", "topics": [ "grabMzmlEncodingData" ] }, { "page": "grabMzmlMetadata", "title": "Helper function to extract mzML file metadata", "topics": [ "grabMzmlMetadata" ] }, { "page": "grabMzmlMS1", "title": "Extract the MS1 data from an mzML nodeset", "topics": [ "grabMzmlMS1" ] }, { "page": "grabMzmlMS2", "title": "Extract the MS2 data from an mzML nodeset", "topics": [ "grabMzmlMS2" ] }, { "page": "grabMzmlMS3", "title": "Extract the MS3 data from an mzML nodeset", "topics": [ "grabMzmlMS3" ] }, { "page": "grabMzxmlBPC", "title": "Grab the BPC or TIC from a file", "topics": [ "grabMzxmlBPC" ] }, { "page": "grabMzxmlData", "title": "Get mass-spectrometry data from an mzXML file", "topics": [ "grabMzxmlData" ] }, { "page": "grabMzxmlEncodingData", "title": "Helper function to extract mzXML file metadata", "topics": [ "grabMzxmlEncodingData" ] }, { "page": "grabMzxmlMetadata", "title": "Helper function to extract mzXML file metadata", "topics": [ "grabMzxmlMetadata" ] }, { "page": "grabMzxmlMS1", "title": "Extract the MS1 data from an mzXML nodeset", "topics": [ "grabMzxmlMS1" ] }, { "page": "grabMzxmlMS2", "title": "Extract the MS2 data from an mzXML nodeset", "topics": [ "grabMzxmlMS2" ] }, { "page": "grabMzxmlMS3", "title": "Extract the MS3 data from an mzXML nodeset", "topics": [ "grabMzxmlMS3" ] }, { "page": "grabMzxmlSpectraMzInt", "title": "Extract the mass-to-charge data from the spectra of an mzXML nodeset", "topics": [ "grabMzxmlSpectraMzInt" ] }, { "page": "grabMzxmlSpectraPremz", "title": "Extract the precursor mass from the spectra of an mzXML nodeset", "topics": [ "grabMzxmlSpectraPremz" ] }, { "page": "grabMzxmlSpectraRt", "title": "Extract the retention time from the spectra of an mzXML nodeset", "topics": [ "grabMzxmlSpectraRt" ] }, { "page": "grabMzxmlSpectraVoltage", "title": "Extract the collision energies from the spectra of an mzXML nodeset", "topics": [ "grabMzxmlSpectraVoltage" ] }, { "page": "grabSpectraInt", "title": "Extract the intensity information from the spectra of an mzML nodeset", "topics": [ "grabSpectraInt" ] }, { "page": "grabSpectraMz", "title": "Extract the mass-to-charge data from the spectra of an mzML nodeset", "topics": [ "grabSpectraMz" ] }, { "page": "grabSpectraPremz", "title": "Extract the precursor mass from the spectra of an mzML nodeset", "topics": [ "grabSpectraPremz" ] }, { "page": "grabSpectraRt", "title": "Extract the retention time from the spectra of an mzML nodeset", "topics": [ "grabSpectraRt" ] }, { "page": "grabSpectraVoltage", "title": "Extract the collision energies from the spectra of an mzML nodeset", "topics": [ "grabSpectraVoltage" ] }, { "page": "minifyMSdata", "title": "Shrink MS data by including only data points near masses of interest", "topics": [ "minifyMSdata" ] }, { "page": "minifyMzml", "title": "Shrink mzML files by including only data points near masses of interest", "topics": [ "minifyMzml" ] }, { "page": "minifyMzxml", "title": "Shrink mzXML files by including only data points near masses of interest", "topics": [ "minifyMzxml" ] }, { "page": "msdata_connection", "title": "S3 constructor for msdata_connection", "topics": [ "msdata_connection" ] }, { "page": "mz_group", "title": "Group m/z values into bins of a specified ppm width", "topics": [ "mz_group" ] }, { "page": "node2dt", "title": "Convert node to data.table", "topics": [ "node2dt" ] }, { "page": "pmppm", "title": "Plus/minus parts per million", "topics": [ "pmppm" ] }, { "page": "print.msdata_connection", "title": "S3 print option for msdata_connection objects", "topics": [ "print.msdata_connection" ] }, { "page": "qplotMS1data", "title": "Quick plot for MS data", "topics": [ "qplotMS1data" ] }, { "page": "tmzmlMaker", "title": "Maker of tmzML documents", "topics": [ "tmzmlMaker" ] }, { "page": "trapz", "title": "Trapezoidal integration of mass-spec retention time / intensity values", "topics": [ "trapz" ] } ], "_readme": "https://github.com/wkumler/rams/raw/HEAD/README.md", "_rundeps": [ "base64enc", "cli", "data.table", "rlang", "xml2" ], "_vignettes": [ { "source": "speed_size_comparison.Rmd", "filename": "speed_size_comparison.html", "title": "Benchmarking - RaMS, MSnBase, Spectra, Arrow, and SQL", "author": "William Kumler", "engine": "knitr::rmarkdown", "headings": [ "Intro", "Original MSnExp", "New onDiskMSnExp infrastructure", "Spectra package", "RaMS package", "tmzML files", "Arrow package", "SQL(ite)", "DuckDB", "MS data transformation timings", "MS data query timings", "Multiple chromatograms", "MS object sizing info", "Summary" ], "created": "2023-12-12 20:57:07", "modified": "2024-10-09 00:12:39", "commits": 7 }, { "source": "Intro-to-RaMS.Rmd", "filename": "Intro-to-RaMS.html", "title": "Intro to RaMS", "engine": "knitr::rmarkdown", "headings": [ "Basic RaMS usage", "TICs, BPCs, and metadata", "Adding a column: MS1 data", "Moving along: MSn data", "Continuing: chromatograms!", "Advanced RaMS usage", "Saving space: EICs and rtrange", "Speeding things up", "Finer control: grabMzmlData, grabMzxmlData", "The nitty-gritty details" ], "created": "2021-03-16 00:55:24", "modified": "2024-09-19 18:48:39", "commits": 17 }, { "source": "Intro-to-tmzML.Rmd", "filename": "Intro-to-tmzML.html", "title": "Introduction to the tmzML file type", "engine": "knitr::rmarkdown", "headings": [ "What is tmzML?", "Why tmzML?", "Getting started with tmzML documents", "Why not tmzML?", "tmzML internals" ], "created": "2022-04-08 19:28:35", "modified": "2024-10-09 00:12:39", "commits": 10 }, { "source": "Minifying-files-with-RaMS.Rmd", "filename": "Minifying-files-with-RaMS.html", "title": "Minifying files with RaMS", "engine": "knitr::rmarkdown", "headings": [], "created": "2022-04-08 19:45:14", "modified": "2024-09-20 22:05:26", "commits": 10 }, { "source": "RaMS-and-friends.Rmd", "filename": "RaMS-and-friends.html", "title": "RaMS and friends", "engine": "knitr::rmarkdown", "headings": [ "Standard export to CSV", "Fancier export to Excel", "Exporting to SQL database", "Interfacing with Python via reticulate", "R code chunk:", "Python code chunk:" ], "created": "2021-01-31 22:09:31", "modified": "2024-03-03 02:04:15", "commits": 11 } ], "_score": 8.895422546039407, "_indexed": true, "_nocasepkg": "rams", "_universes": [ "wkumler" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.3", "date": "2026-07-15T06:32:31.000Z", "distro": "resolute", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/5a95674f74cf4c01cb6c611c91f6d3117707e2d4adcaebfa62c195faed62139b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.6.1", "os": "linux", "version": "1.4.3", "date": "2026-07-15T06:33:37.000Z", "distro": "resolute", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/207151726cf5d45953e74595f18a2576c529994743974e5e418bf78f59f81ad5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.5.3", "os": "mac", "version": "1.4.3", "date": "2026-07-15T06:32:31.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/f5e7967c8cee32a42c13074f2afa3d1fe893231fde2b893f9c82b1a7aee87882", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.6.1", "os": "mac", "version": "1.4.3", "date": "2026-07-15T06:31:41.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/5336c8ed908be73a3b9c46331633eda117cbbecbebc77c90be54f52759c5a80e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.3", "date": "2026-07-15T06:32:39.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/5c6c409c30b05ce68c82ae12f98a4f406022bde78375fd18b5c9659d5abb27fb", "status": "success", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.7.0", "os": "win", "version": "1.4.3", "date": "2026-07-15T06:31:16.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/a9456b61cecde902a8309fe238349f966bc61cb57bb65a6318b95231fa306be4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.5.3", "os": "win", "version": "1.4.3", "date": "2026-07-15T06:31:17.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/4f97b265d6927c9f5a9edfd18a92b787e39154e4634bd0803dc0c409929dc3a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" }, { "r": "4.6.1", "os": "win", "version": "1.4.3", "date": "2026-07-15T06:31:23.000Z", "commit": "f6f3bb0b8540fbea777672ad1d55cb092466401d", "fileid": "https://r2.ropensci.org/bbfce71f793cb93d548dd8d797327a8409355c77945a1e98fd28c2319fb65a4c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/wkumler/actions/runs/29394151080" } ] }