{ "_id": "6a0f61f7acfb0bcc41c5c15f", "Package": "SIMAT", "Type": "Package", "Title": "GC-SIM-MS data processing and alaysis tool", "Version": "1.45.0", "Date": "2018-08-02", "Author": "M. R. Nezami Ranjbar ", "Maintainer": "M. R. Nezami Ranjbar ", "Description": "This package provides a pipeline for analysis of GC-MS\ndata acquired in selected ion monitoring (SIM) mode. The tool\nalso provides a guidance in choosing appropriate fragments for\nthe targets of interest by using an optimization algorithm.\nThis is done by considering overlapping peaks from a provided\nlibrary by the user.", "License": "GPL-2", "biocViews": "ImmunoOncology, Software, Metabolomics, MassSpectrometry", "URL": "http://omics.georgetown.edu/SIMAT.html", "Config/pak/sysreqs": "libicu-dev libnetcdf-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:48 UTC", "RemoteUrl": "https://github.com/bioc/SIMAT", "RemoteRef": "HEAD", "RemoteSha": "eec66a6a75c8c328ec20efe97987f3916707aef4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 10:41:29 UTC", "User": "root" }, "MD5sum": "3671bc7edb040a5a26b8da019125a52e", "_user": "bioc", "_type": "src", "_file": "SIMAT_1.45.0.tar.gz", "_fileid": "5d1079e592596bee4e46251307aabfad07b5126ac57ecf942830875da4361f5d", "_filesize": 1195650, "_sha256": "5d1079e592596bee4e46251307aabfad07b5126ac57ecf942830875da4361f5d", "_created": "2026-05-21T10:41:29.000Z", "_published": "2026-05-21T19:50:15.730Z", "_jobs": [ { "job": 77255766735, "time": 133, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7133645232" }, { "job": 77255766619, "time": 232, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7133677355" }, { "job": 77255767133, "time": 246, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7133681895" }, { "job": 77255767039, "time": 121, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7133803506" }, { "job": 77255766778, "time": 105, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7133839496" }, { "job": 77255765822, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7133600456" }, { "job": 77255766268, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7145687327" }, { "job": 77255766718, "time": 128, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7133643674" }, { "job": 77255767113, "time": 93, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7133632614" }, { "job": 77255766695, "time": 110, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7133638318" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26220879210", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SIMAT", "_commit": { "id": "eec66a6a75c8c328ec20efe97987f3916707aef4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380048 }, "_maintainer": { "name": "M. 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true }, { "name": "RItable", "title": "Extracted RI standard information from a 'csv' file.", "object": "RItable", "file": "RItable.rda", "class": [ "data.frame" ], "fields": [ "rt", "ri" ], "rows": 13, "table": true, "tojson": true }, { "name": "Run", "title": "Extracted peaks from one SIM run.", "object": "Run", "file": "Run.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "target.table", "title": "Extracted target information from a 'csv' file.", "object": "target.table", "file": "target.table.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Targets", "title": "Targets information in a list.", "object": "Targets", "file": "Targets.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "SIMAT-package", "title": "This package is for processing GC-SIM-MS data", "topics": [ "SIMAT-package", "SIMAT" ] }, { "page": "getEIC", "title": "Get the EIC of a peak", "topics": [ "getEIC" ] }, { "page": "getPeak", "title": "Get all peaks corresponding to targets in several runs", "topics": [ "getPeak" ] }, { "page": "getPeakScore", "title": "Calculate the similarity score for all peaks", "topics": [ "getPeakScore" ] }, { "page": "getRI", "title": "Generate a calibration function", "topics": [ "getRI" ] }, { "page": "getRIStandard", "title": "Get the RI standard information", "topics": [ "getRIStandard" ] }, { "page": "getScore", "title": "Calculate similarity score for a peak", "topics": [ "getScore" ] }, { "page": "getTarget", "title": "Get target information", "topics": [ "getTarget" ] }, { "page": "getTargetTable", "title": "Get target table information", "topics": [ "getTargetTable" ] }, { "page": "Library", "title": "Extracted compound information from an MSL library.", "topics": [ "Library" ] }, { "page": "optFrag", "title": "Fragment selection through optimization", "topics": [ "optFrag" ] }, { "page": "plotEIC", "title": "Plotting EIC of one peak", "topics": [ "plotEIC" ] }, { "page": "plotTIC", "title": "Plotting TIC of one run", "topics": [ "plotTIC" ] }, { "page": "putTargetTable", "title": "Put target table information", "topics": [ "putTargetTable" ] }, { "page": "readCDF", "title": "Read raw mass spectrometry data in netCDF files", "topics": [ "readCDF" ] }, { "page": "readMSL", "title": "Read mass spectral library (MSL) files", "topics": [ "readMSL" ] }, { "page": "RItable", "title": "Extracted RI standard information from a 'csv' file.", "topics": [ "RItable" ] }, { "page": "Run", "title": "Extracted peaks from one SIM run.", "topics": [ "Run" ] }, { "page": "target.table", "title": "Extracted target information from a 'csv' file.", "topics": [ "target.table" ] }, { "page": "Targets", "title": "Targets information in a list.", "topics": [ "Targets" ] }, { "page": "writeMSL", "title": "Write targets information into a file with mass spectral library (MSL) format.", "topics": [ "writeMSL" ] }, { "page": "writeResult", "title": "Write analysis results to file.", "topics": [ "writeResult" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "biocmake", "cli", "cpp11", "dir.expiry", "farver", "filelock", "generics", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "magrittr", "mzR", "ncdf4", "plyr", "ProtGenerics", "R6", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "S7", "scales", "stringi", "stringr", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "SIMAT-vignette.Rnw", "filename": "SIMAT-vignette.pdf", "title": "SIMAT Usage", "engine": "utils::Sweave", "headings": [], "created": "2015-03-13 17:25:56", "modified": "2018-08-03 16:28:26", "commits": 4 } ], "_score": 4.2552725051033065, "_indexed": true, "_nocasepkg": "simat", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-05-21T10:44:59.000Z", "distro": "noble", "commit": "eec66a6a75c8c328ec20efe97987f3916707aef4", "fileid": 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