{ "_id": "6a499dd93431763c10450212", "Package": "flagme", "Version": "1.69.0", "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.r-universe.dev", "Date/Publication": "2026-04-28 12:33:35 UTC", "RemoteUrl": "https://github.com/bioc/flagme", "RemoteRef": "HEAD", "RemoteSha": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-21 09:40:44 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "flagme_1.69.0.tar.gz", "_fileid": "https://r2.ropensci.org/568ef035edbe3c68d945f7c90924521c2124b3ceee5228bf02ed8d6f979b913b", "_filesize": 633346, "_sha256": "568ef035edbe3c68d945f7c90924521c2124b3ceee5228bf02ed8d6f979b913b", "_expires": "2026-10-12T23:57:11.000Z", "_created": "2026-06-21T09:40:44.000Z", "_published": "2026-07-04T23:57:13.070Z", "_bioccheck": { "error": 1, "warning": 5, "note": 15 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627", "_status": "success", "_upstream": "https://github.com/bioc/flagme", "_commit": { "id": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379615 }, "_maintainer": { "name": "Mark Robinson", "email": "riccardo.romoli@unifi.it" }, "_distro": "noble", "_jobs": [ { "job": 85177218483, "time": 236, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7785280510" }, { "job": 85177218493, "time": 638, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7774132294" }, { "job": 85177218548, "time": 868, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7774160360" }, { "job": 85177218626, "time": 635, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7774131922" }, { "job": 85177218567, "time": 739, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7774144303" }, { "job": 85177218629, "time": 412, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7774102810" }, { "job": 85177218647, "time": 939, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7774169497" }, { "job": 85177218508, "time": 509, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7774114616" }, { "job": 85177218477, "time": 1515, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7785672024" }, { "job": 85177218402, "time": 472, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7774048830" }, { "job": 85177218487, "time": 172, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7774071202" }, { "job": 85177218533, "time": 1029, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7774180144" }, { "job": 85177218536, "time": 1077, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7774185800" }, { "job": 85177218458, "time": 952, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7774170786" } ], "_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": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_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", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_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/HEAD/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": true, "_nocasepkg": "flagme", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.69.0", "date": "2026-06-21T09:44:34.000Z", "distro": "noble", "arch": "aarch64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/0a1c9fd9d8a6f51157ae826b1e1ed473b6d2a7b9a038b879da1b38847f507e87", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.7.0", "os": "linux", "version": "1.69.0", "date": "2026-06-21T09:45:56.000Z", "distro": "noble", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/e66a31102cbad584ae2a87305c1e1c8e7cd7f4d844b08688ac23cb839e806f96", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "linux", "version": "1.69.0", "date": "2026-06-21T09:44:26.000Z", "distro": "noble", "arch": "aarch64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/c71a4744a123b821c5ca91e4482369856b2e6968ca07fa706c98b657738aecee", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "linux", "version": "1.69.0", "date": "2026-06-21T09:45:19.000Z", "distro": "noble", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/b6332d47bc11eaa42c91032a4b3169e44c85b8e7207394a7fa7e2ca0497a0163", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.5.3", "os": "mac", "version": "1.69.0", "date": "2026-06-21T09:43:01.000Z", "arch": "aarch64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/a076b2ea4ef56fc4ed08cd93aa1484530c21c3a8d094d98ffde910bc88e9d3c8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.5.3", "os": "mac", "version": "1.69.0", "date": "2026-06-21T09:45:16.000Z", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/a7d45a627e966d812c2cd8f9cca61113427769cb2ed36ba4e2c81decab92116d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "mac", "version": "1.69.0", "date": "2026-06-21T09:43:06.000Z", "arch": "aarch64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/f7a227802683bfe1908e5e2eabd964d17ca82376c06878ad7562bed11e377663", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "mac", "version": "1.69.0", "date": "2026-06-22T07:03:23.000Z", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/05d971836187cf480ff66db81f17082309f9d06594c6240904f633bcdc560994", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "wasm", "version": "1.69.0", "date": "2026-06-21T09:44:30.000Z", "arch": "emscripten", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/12c010f418bdda7d2e5c0234bb041e8f54f689e39f0548dd9cc694150a3cec0b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.7.0", "os": "win", "version": "1.69.0", "date": "2026-06-21T09:43:12.000Z", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/72885cf7b195e52b61ca8dc825db0dac3949adae4e46af7cd6b18bf5845de8a1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.5.3", "os": "win", "version": "1.69.0", "date": "2026-06-21T09:43:09.000Z", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/a2ea7498d857a836a0a56be4d3fb7249826b6065dbed095064435f606938a993", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" }, { "r": "4.6.0", "os": "win", "version": "1.69.0", "date": "2026-06-21T09:43:20.000Z", "arch": "x86_64", "commit": "0272058b6408ec90ddf5ffd980e3e5528a9e92a8", "fileid": "https://r2.ropensci.org/43c1e6fda17f19d9a02763a6cfcdfda475b440bf1a9a45b5e32a60e79e3510de", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/27900202627" } ] }