Package: flagme 1.69.0

Mark Robinson

flagme: Analysis of Metabolomics GC/MS Data

Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.

Authors:Mark Robinson <[email protected]>, Riccardo Romoli <[email protected]>

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manual.pdf |manual.html✨
card.svg |card.png
flagme/json (API)
NEWS

# Install 'flagme' in R:
install.packages('flagme', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:flagme-1.69.0(bioc 3.24)flagme-1.68.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

differentialexpressionmassspectrometry

4.30 score 2 scripts 394 downloads 1 mentions 33 exports 156 dependencies

Last updated from:0272058b64. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

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macos-oldrel-arm64WARNING418
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Exports:addAMDISPeaksaddChromaTOFPeaksaddXCMSPeaksbetweenAlignmentcalcTimeDiffsclusterAlignmentcorPrtdistToLibdpdynRTexportSpectragatherInfoheadToTailPlotimportSpecimputePeaksmatchSpecmultipleAlignmentndpRTnormDotProductparseChromaTOFparseELUpeaksAlignmentpeaksDatasetplotAlignedFragsplotAlignmentplotChromplotClustAlignmentplotFragsplotImageprogressiveAlignmentretFatMatrixrmaFitUnitshow

Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelbitopsbslibcachemCAMERAcaToolscheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdir.expirydoParalleldplyrevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgcspikelitegenericsGenomicRangesggplot2gluegplotsgraphgridExtragtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4nnetopensslotelpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchPTModspurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfosnowSparseArraySparseMSpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryaml

\texttt{flagme}: Fragment-level analysis of \ GC-MS-based metabolomics data

Rendered fromflagme.Rnwusingutils::Sweaveon May 22 2026.

Last update: 2023-02-07
Started: 2013-11-01

Using flagme -- Fragment-level analysis of GC-MS-based metabolomics data

Rendered fromflagme-knitr.Rnwusingutils::Sweaveon May 22 2026.

Last update: 2023-02-07
Started: 2021-10-26

Readme and manuals

Help Manual

Help pageTopics
Add AMDIS peak detection resultsaddAMDISPeaks
Add ChromaTOF peak detection resultsaddChromaTOFPeaks
addXCMSPeaksaddXCMSPeaks
Data Structure for "between" alignment of many GCMS samplesbetweenAlignment betweenAlignment-class betweenAlignment-method betweenAlignment-show show,
Calculate retention time shifts from profile alignmentscalcTimeDiffs
Data Structure for a collection of all pairwise alignments of GCMS runsclusterAlignment clusterAlignment-class clusterAlignment-plot clusterAlignment-show plot,clusterAlignment,ANY-method plot,clusterAlignment-method show,clusterAlignment-method
Retention Time Penalized CorrelationcorPrt
deDuperdeDuper
distToLibdistToLib
Dynamic programming algorithm, given a similarity matrixdp
dynRTdynRT
A class descriptioneitherMatrix-class
exportSpectraexportSpectra
Gathers abundance informations from an alignmentgatherInfo
Head to tail plotheadToTailPlot
importSpecimportSpec
Imputatin of locations of peaks that were undetectedimputePeaks
matchSpecmatchSpec
Data Structure for multiple alignment of many GCMS samplesmultipleAlignment multipleAlignment-class multipleAlignment-class, multipleAlignment-method multipleAlignment-show,
Retention Time Penalized Normalized Dot ProductndpRT
Normalized Dot ProductnormDotProduct
Parser for ChromaTOF filesparseChromaTOF
Parser for ELU filesparseELU
Data Structure for pairwise alignment of 2 GCMS samplespeaksAlignment peaksAlignment-class peaksAlignment-plot peaksAlignment-show plot,peaksAlignment,ANY-method plot,peaksAlignment-method show,peaksAlignment-method
Data Structure for raw GCMS data and peak detection resultspeaksDataset peaksDataset-class peaksDataset-plot peaksDataset-show plot,peaksDataset,ANY-method plot,peaksDataset-method show,peaksDataset-method
plotAlignedFragsplotAlignedFrags
plotAlignmentplotAlignment,peaksAlignment-method
Plotting functions for GCMS data objectsplotChrom,peaksDataset-method
plotClustAlignmentplotClustAlignment,clusterAlignment-method
plotFragsplotFrags
Plot of images of GCMS dataplotImage plotImage,peaksDataset-method
Data Structure for progressive alignment of many GCMS samplesprogressiveAlignment progressiveAlignment-class progressiveAlignment-show show,progressiveAlignment-method
retFatMatrixretFatMatrix
Fits a robust linear model (RLM) for one metabolitermaFitUnit
Store the raw data and optionally, information regarding signal peaks for a number of GCMS runsshow,multipleAlignment-method