{ "_id": "6a2e74293efcd9bda4314b4c", "Package": "rtmsEcho", "Title": "Extract and Analyze EchoMS Data from Sciex Wiff Files", "Version": "0.2.4", "Authors@R": "c(\nperson(\"Mary Ashley\", \"Rimmer\", email=\"maryashley.rimmer@stjude.org\", role = c(\"aut\")),\nperson(\"Nathaniel\", \"Twarog\", email=\"nathaniel.twarog@stjude.org\", role = c(\"aut\", \"cre\")),\nperson(\"Lei\", \"Yang\", email=\"lei.yang@stjude.org\", role = c(\"aut\")))", "Description": "Read raw and processed data from acoustic ejection mass\nspectrometry (AEMS) files produced by the Sciex EchoMS\ninstrument. Includes functions to create interactive reader\nobjects, extract raw intensity measurements, mass spectra, and\nfully-processed mass-transition intensity areas. Methods for\ndata processing and analysis are described in Rimmer et al.\n(2025) . Supports both\nmultiple reaction monitoring (MRM) and full-scan (neutral loss\nand precursor ion) data formats.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "LazyData": "true", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-14 09:24:54 UTC", "User": "root" }, "Author": "Mary Ashley Rimmer [aut], Nathaniel Twarog [aut, cre], Lei Yang\n[aut]", "Maintainer": "Nathaniel Twarog ", "Repository": "https://nathanieltwarog.r-universe.dev", "Date/Publication": "2026-01-14 18:10:02 UTC", "RemoteUrl": "https://github.com/cran/rtmsEcho", "RemoteRef": "HEAD", "RemoteSha": "f05999c5d704e746c47fd8012a5a96d34e14c751", "MD5sum": "98a5dd405d57d92cd86cbb8dee3ab900", "_user": "nathanieltwarog", "_type": "src", "_file": "rtmsEcho_0.2.4.tar.gz", "_fileid": "45c11abe1000d31d59186d6a784907d30c03fcf4ea345dbe65a6179651ba7355", "_filesize": 285312, "_sha256": "45c11abe1000d31d59186d6a784907d30c03fcf4ea345dbe65a6179651ba7355", "_created": "2026-06-14T09:24:54.000Z", "_published": "2026-06-14T09:28:09.785Z", "_distro": "noble", "_jobs": [ { "job": 81266123582, "time": 104, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7619629350" }, { "job": 81266123591, "time": 110, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7619629176" }, { "job": 81266123588, "time": 160, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7619631627" }, { "job": 81266123577, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7619631096" }, { "job": 81265931360, "time": 182, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7619614111" }, { "job": 81266123573, "time": 91, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7619626509" }, { "job": 81266123585, "time": 99, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7619627452" }, { "job": 81266123569, "time": 75, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7619624495" }, { "job": 81266123568, "time": 68, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7619624221" } ], "_buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/rtmsEcho", "_commit": { "id": "f05999c5d704e746c47fd8012a5a96d34e14c751", "author": "Nathaniel Twarog ", "committer": "cran-robot ", "message": "version 0.2.4\n", "time": 1768414202 }, "_maintainer": { "name": "Nathaniel Twarog", "email": "nathaniel.twarog@stjude.org", "login": "nathanieltwarog", "description": "", "uuid": 17708163 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "rtms", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-03", "n": 1 } ], "_tags": [ { "name": "0.2.4", "date": "2026-01-14" } ], "_stars": 0, "_contributors": [ { "user": "nathanieltwarog", "count": 1, "uuid": 17708163 } ], "_userbio": { "uuid": 17708163, "type": "user", "name": "Nathaniel Twarog", "followers": 1 }, "_downloads": { "count": 138, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rtmsEcho" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/rtmsEcho.html", "manual.pdf" ], "_realowner": "nathanieltwarog", "_cranurl": false, "_releases": [ { "version": "0.2.4", "date": "2026-01-14" } ], "_exports": [ "getAllFullScanAreas", "getAllFullScanSpectra", "getAllMRMAreas", "getAllTIC", "getFullScanAreas", "getFullScanData", "getFullScanSpectrum", "getMRMAreas", "getMRMChromatograms", "getTIC", "getWiffShots", "measureEjections", "newWiffReader", "processAllFullScanAreas", "processAllMRMAreas" ], "_datasets": [ { "name": "exampleWiff", "title": "Example wiff reader object", "object": "exampleWiff", "class": [ "rtmsWiffReaderMRM", "rtmsWiffReader" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "exampleWiff", "title": "Example wiff reader object", "topics": [ "exampleWiff" ] }, { "page": "getAllFullScanAreas", "title": "Get the total area for given masses for all wells", "topics": [ "getAllFullScanAreas" ] }, { "page": "getAllFullScanSpectra", "title": "Extract mass spectra for all wells", "topics": [ "getAllFullScanSpectra" ] }, { "page": "getAllMRMAreas", "title": "Extract the peak areas for MRM mass transitions for all wells", "topics": [ "getAllMRMAreas" ] }, { "page": "getAllTIC", "title": "Extract all total ion chromatograms from a Wiff file", "topics": [ "getAllTIC" ] }, { "page": "getFullScanAreas", "title": "Get the total area for given masses for a particular well", "topics": [ "getFullScanAreas" ] }, { "page": "getFullScanData", "title": "Extract raw Wiff full scan data", "topics": [ "getFullScanData" ] }, { "page": "getFullScanSpectrum", "title": "Extract a full mass spectrum for a given well", "topics": [ "getFullScanSpectrum" ] }, { "page": "getMRMAreas", "title": "Extract the peak areas for MRM mass transitions for a given well", "topics": [ "getMRMAreas" ] }, { "page": "getMRMChromatograms", "title": "Extract full chromatograms for each mass transition", "topics": [ "getMRMChromatograms" ] }, { "page": "getTIC", "title": "Extract a total ion chromatogram (TIC) from a Wiff file", "topics": [ "getTIC" ] }, { "page": "getWiffShots", "title": "List of Shot Names in a given Wiff File", "topics": [ "getWiffShots" ] }, { "page": "measureEjections", "title": "Measure total ion chromatogram peaks to estimate ejection time", "topics": [ "measureEjections", "measureEjections.default", "measureEjections.rtmsWiffReader" ] }, { "page": "newWiffReader", "title": "Open a Sciex EchoMS wiff File for Reading", "topics": [ "newWiffReader" ] }, { "page": "processAllFullScanAreas", "title": "Fully process a Full Scan Wiff and scan File", "topics": [ "processAllFullScanAreas" ] }, { "page": "processAllMRMAreas", "title": "Process an MRM file in total", "topics": [ "processAllMRMAreas" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "rtms", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 1, "_indexed": true, "_nocasepkg": "rtmsecho", "_universes": [ "nathanieltwarog" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.4", "date": "2026-06-14T09:26:50.000Z", "distro": "noble", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "339747712cafaf5f31ac461aafad6388aff0d140a40d4644343934b1ae880244", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.6.0", "os": "linux", "version": "0.2.4", "date": "2026-06-14T09:26:49.000Z", "distro": "noble", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "6f071f83885c3e99e539aedd6de8700dfe151a88f7ad38c120b15573f25d6714", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.5.3", "os": "mac", "version": "0.2.4", "date": "2026-06-14T09:27:09.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "f9bc43aa78d68c6fe6ac681689129d6f8aa0ad3bcc25d4223a8387339b52b05b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.6.0", "os": "mac", "version": "0.2.4", "date": "2026-06-14T09:27:03.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "521c4b11f87bfbabf15ab84d5b71c9963e8afd3a659735161ccb12b460613288", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.4", "date": "2026-06-14T09:26:41.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "e0e74ef7188f709139c80b16ab2081ac546f581dca9454626c7106e6b0fd183f", "status": "success", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.7.0", "os": "win", "version": "0.2.4", "date": "2026-06-14T09:26:22.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "f6088dc8990fbd65d9db9e3da51dba4ac746962a0d8f408fd5857957f47b806b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.5.3", "os": "win", "version": "0.2.4", "date": "2026-06-14T09:26:12.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "6b0a335c83b0cdd41954c6558dcc1718885ad8e2b19ca4298430682c82348a28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" }, { "r": "4.6.0", "os": "win", "version": "0.2.4", "date": "2026-06-14T09:26:08.000Z", "commit": "f05999c5d704e746c47fd8012a5a96d34e14c751", "fileid": "d0cc319038ac66cc20a24b6baac7a67c0457f474cf9a531987888e49ac710ded", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nathanieltwarog/actions/runs/27494487324" } ] }