{ "_id": "6a194bfaacfb0bcc41ddd303", "Package": "flagme", "Version": "1.68.0", "Date": "2015/04/06", "Title": "Analysis of Metabolomics GC/MS Data", "Author": "Mark Robinson , Riccardo Romoli\n", "Maintainer": "Mark Robinson , Riccardo Romoli\n", "Description": "Fragment-level analysis of gas\nchromatography-massspectrometry metabolomics data.", "License": "LGPL (>= 2)", "Collate": "0classes.R clusterAlignment.R init.R multipleAlignment.R\npeaksAlignment.R progressiveAlignment.R betweenAlignment.R dp.R\nmetrics.R parse.R peaksDataset.R gatherInfo.R plotFragments.R\nrmaFitUnit.R addXCMSPeaks.R retFatMatrix.R exportSpectra.R\nimportSpectra.R", "biocViews": "DifferentialExpression, MassSpectrometry", "RoxygenNote": "7.2.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:33:35 UTC", "RemoteUrl": "https://github.com/bioc/flagme", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-29 07:04:37 UTC", "User": "root" }, "MD5sum": "2d6fae4bdfcbd8e522c906848ba11e5e", "_user": "bioc-release", "_type": "src", "_file": "flagme_1.68.0.tar.gz", "_fileid": "ef249163351dc741ba78c291291dfc4553f334f3b89c54663589570f1bf27082", "_filesize": 628888, "_sha256": "ef249163351dc741ba78c291291dfc4553f334f3b89c54663589570f1bf27082", "_created": "2026-05-29T07:04:37.000Z", "_published": "2026-05-29T08:19:06.365Z", "_jobs": [ { "job": 78454213722, "time": 228, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7285080098" }, { "job": 78454213781, "time": 642, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7285186278" }, { "job": 78454213847, "time": 840, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7285239546" }, { "job": 78454213755, "time": 702, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7285202836" }, { "job": 78454213800, "time": 823, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7285234911" }, { "job": 78454213757, "time": 540, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7286189972" }, { "job": 78454213801, "time": 893, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7286188506" }, { "job": 78454213852, "time": 472, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7286171489" }, { "job": 78454213728, "time": 1107, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7286249627" }, { "job": 78453267354, "time": 443, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285023734" }, { "job": 78454213768, "time": 176, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285068029" }, { "job": 78454213766, "time": 1168, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7285332453" }, { "job": 78454213726, "time": 1053, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7285297959" }, { "job": 78454213714, "time": 1088, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7285309477" } ], "_bioccheck": { "error": 1, "warning": 4, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/flagme", "_commit": { "id": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379615 }, "_maintainer": { "name": "Mark Robinson", "email": "riccardo.romoli@unifi.it" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "gcspikelite", "role": "Depends" }, { "package": "xcms", "role": "Depends" }, { "package": "CAMERA", "role": "Depends" }, { "package": "gplots", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SparseM", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.69.0", "bioc": "3.24" }, { "branch": "release", "version": "1.68.0", "bioc": "3.23" } ], "_topics": [ "differentialexpression", "massspectrometry" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 394, "source": "https://www.bioconductor.org/packages/stats/bioc/flagme" }, "_mentions": 1, "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flagme.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "addAMDISPeaks", "addChromaTOFPeaks", "addXCMSPeaks", "betweenAlignment", "calcTimeDiffs", "clusterAlignment", "corPrt", "distToLib", "dp", "dynRT", "exportSpectra", "gatherInfo", "headToTailPlot", "importSpec", "imputePeaks", "matchSpec", "multipleAlignment", "ndpRT", "normDotProduct", "parseChromaTOF", "parseELU", "peaksAlignment", "peaksDataset", "plotAlignedFrags", "plotAlignment", "plotChrom", "plotClustAlignment", "plotFrags", "plotImage", "progressiveAlignment", "retFatMatrix", "rmaFitUnit", "show" ], "_help": [ { "page": "addAMDISPeaks", "title": "Add AMDIS peak detection results", "topics": [ "addAMDISPeaks" ] }, { "page": "addChromaTOFPeaks", "title": "Add ChromaTOF peak detection results", "topics": [ "addChromaTOFPeaks" ] }, { "page": "addXCMSPeaks", "title": "addXCMSPeaks", "topics": [ "addXCMSPeaks" ] }, { "page": "betweenAlignment", "title": "Data Structure for \"between\" alignment of many GCMS samples", "topics": [ "betweenAlignment", "betweenAlignment-class", "betweenAlignment-method", "betweenAlignment-show", "show," ] }, { "page": "calcTimeDiffs", "title": "Calculate retention time shifts from profile alignments", "topics": [ "calcTimeDiffs" ] }, { "page": "clusterAlignment", "title": "Data Structure for a collection of all pairwise alignments of GCMS runs", "topics": [ "clusterAlignment", "clusterAlignment-class", "clusterAlignment-plot", "clusterAlignment-show", "plot,clusterAlignment,ANY-method", "plot,clusterAlignment-method", "show,clusterAlignment-method" ] }, { "page": "corPrt", "title": "Retention Time Penalized Correlation", "topics": [ "corPrt" ] }, { "page": "deDuper", "title": "deDuper", "topics": [ "deDuper" ] }, { "page": "distToLib", "title": "distToLib", "topics": [ "distToLib" ] }, { "page": "dp", "title": "Dynamic programming algorithm, given a similarity matrix", "topics": [ "dp" ] }, { "page": "dynRT", "title": "dynRT", "topics": [ "dynRT" ] }, { "page": "eitherMatrix-class", "title": "A class description", "topics": [ "eitherMatrix-class" ] }, { "page": "exportSpectra", "title": "exportSpectra", "topics": [ "exportSpectra" ] }, { "page": "gatherInfo", "title": "Gathers abundance informations from an alignment", "topics": [ "gatherInfo" ] }, { "page": "headToTailPlot", "title": "Head to tail plot", "topics": [ "headToTailPlot" ] }, { "page": "importSpec", "title": "importSpec", "topics": [ "importSpec" ] }, { "page": "imputePeaks", "title": "Imputatin of locations of peaks that were undetected", "topics": [ "imputePeaks" ] }, { "page": "matchSpec", "title": "matchSpec", "topics": [ "matchSpec" ] }, { "page": "multipleAlignment-class", "title": "Data Structure for multiple alignment of many GCMS samples", "topics": [ "multipleAlignment", "multipleAlignment-class", "multipleAlignment-class,", "multipleAlignment-method", "multipleAlignment-show," ] }, { "page": "ndpRT", "title": "Retention Time Penalized Normalized Dot Product", "topics": [ "ndpRT" ] }, { "page": "normDotProduct", "title": "Normalized Dot Product", "topics": [ "normDotProduct" ] }, { "page": "parseChromaTOF", "title": "Parser for ChromaTOF files", "topics": [ "parseChromaTOF" ] }, { "page": "parseELU", "title": "Parser for ELU files", "topics": [ "parseELU" ] }, { "page": "peaksAlignment-class", "title": "Data Structure for pairwise alignment of 2 GCMS samples", "topics": [ "peaksAlignment", "peaksAlignment-class", "peaksAlignment-plot", "peaksAlignment-show", "plot,peaksAlignment,ANY-method", "plot,peaksAlignment-method", "show,peaksAlignment-method" ] }, { "page": "peaksDataset", "title": "Data Structure for raw GCMS data and peak detection results", "topics": [ "peaksDataset", "peaksDataset-class", "peaksDataset-plot", "peaksDataset-show", "plot,peaksDataset,ANY-method", "plot,peaksDataset-method", "show,peaksDataset-method" ] }, { "page": "plotAlignedFrags", "title": "plotAlignedFrags", "topics": [ "plotAlignedFrags" ] }, { "page": "plotAlignment-peaksAlignment-method", "title": "plotAlignment", "topics": [ "plotAlignment,peaksAlignment-method" ] }, { "page": "plotChrom-peaksDataset-method", "title": "Plotting functions for GCMS data objects", "topics": [ "plotChrom,peaksDataset-method" ] }, { "page": "plotClustAlignment-clusterAlignment-method", "title": "plotClustAlignment", "topics": [ "plotClustAlignment,clusterAlignment-method" ] }, { "page": "plotFrags", "title": "plotFrags", "topics": [ "plotFrags" ] }, { "page": "plotImage", "title": "Plot of images of GCMS data", "topics": [ "plotImage", "plotImage,peaksDataset-method" ] }, { "page": "progressiveAlignment-class", "title": "Data Structure for progressive alignment of many GCMS samples", "topics": [ "progressiveAlignment", "progressiveAlignment-class", "progressiveAlignment-show", "show,progressiveAlignment-method" ] }, { "page": "retFatMatrix", "title": "retFatMatrix", "topics": [ "retFatMatrix" ] }, { "page": "rmaFitUnit", "title": "Fits a robust linear model (RLM) for one metabolite", "topics": [ "rmaFitUnit" ] }, { "page": "show-multipleAlignment-method", "title": "Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs", "topics": [ "show,multipleAlignment-method" ] } ], "_readme": "https://github.com/bioc/flagme/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bitops", "bslib", "cachem", "CAMERA", "caTools", "checkmate", "cli", "clue", "cluster", "codetools", "colorspace", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "gcspikelite", "generics", "GenomicRanges", "ggplot2", "glue", "gplots", "graph", "gridExtra", "gtable", "gtools", "highr", "Hmisc", "hms", "htmlTable", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "magrittr", "MALDIquant", "MASS", "MassSpecWavelet", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "MsExperiment", "MsFeatures", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "nnet", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "preprocessCore", "prettyunits", "progress", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "R6", "rappdirs", "RBGL", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "rpart", "rstudioapi", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "SparseM", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xcms", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "flagme.Rnw", "filename": "flagme.pdf", "title": "\\texttt{flagme}: Fragment-level analysis of \\ GC-MS-based metabolomics data", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:06:30", "modified": "2023-02-07 13:30:30", "commits": 9 }, { "source": "flagme-knitr.Rnw", "filename": "flagme-knitr.pdf", "title": "Using flagme -- Fragment-level analysis of GC-MS-based metabolomics data", "engine": "utils::Sweave", "headings": [], "created": "2021-10-26 13:08:30", "modified": "2023-02-07 13:30:30", "commits": 2 } ], "_score": 4.301029995663981, "_indexed": false, "_nocasepkg": "flagme", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/flagme", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.68.0", "date": "2026-05-29T07:08:26.000Z", "distro": "noble", "arch": "aarch64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "15d871c7f1d634f0efc5b982af553895c88156a0cb4761300efaa808fc1085ac", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.7.0", "os": "linux", "version": "1.68.0", "date": "2026-05-29T07:08:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "2662ce781e0537179c11104c28818897a6bbb0f84fb707425c470349f37d5b2e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "linux", "version": "1.68.0", "date": "2026-05-29T07:08:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "1dab0610ef4d5c98356d9fa8ffd7da62d52adb3d57e3ce53c0333fb402ef3409", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "linux", "version": "1.68.0", "date": "2026-05-29T07:08:40.000Z", "distro": "noble", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "608dd3b90de9c27cdf5e6465678b1a4be5490a9bc654e9d46e5ba059632769c3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.5.3", "os": "mac", "version": "1.68.0", "date": "2026-05-29T08:07:42.000Z", "arch": "aarch64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "995896c717417cf1b5b828b0af56481dbb2fa23d4683deb7437ddd233f0a30c1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.5.3", "os": "mac", "version": "1.68.0", "date": "2026-05-29T08:03:12.000Z", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "ec23d3485ffcb9817cc325581fd9356204cb99570020eb0dbd9cf528b439a599", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "mac", "version": "1.68.0", "date": "2026-05-29T08:07:33.000Z", "arch": "aarch64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "f0aeec6ec2d7d9095d6a60f3d4a512428864471ad11c8329bddf3cc556d01422", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "mac", "version": "1.68.0", "date": "2026-05-29T08:04:48.000Z", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "d7968e12ab9c0bf2d5275f978e781aa4bc3b43230ab2bc09e1bcde53015a7ef3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "wasm", "version": "1.68.0", "date": "2026-05-29T07:08:24.000Z", "arch": "emscripten", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "a73b10aeee03e27abdf11b2875202c83f0fa718fa5f70ae4590fcd33dfbb12e1", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.7.0", "os": "win", "version": "1.68.0", "date": "2026-05-29T07:07:42.000Z", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "20be3d8dba2276ef25c6112ead8cd0628ae48e4beac9237972e3d66dfb762478", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.5.3", "os": "win", "version": "1.68.0", "date": "2026-05-29T07:07:23.000Z", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "feeb0c02da84740f4008b2fbe9e41f24a0428fc52ea31534ccf7a82cc447897f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" }, { "r": "4.6.0", "os": "win", "version": "1.68.0", "date": "2026-05-29T07:07:16.000Z", "arch": "x86_64", "commit": "e36ee4574dea7c40993ea558676c63fc4f9aa054", "fileid": "0895720a22c1f376f596e3def50cd625c0f3852d8fe25d783f4c35983972679b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26623062678" } ] }