Package: flagme 1.63.0
Mark Robinson
flagme: Analysis of Metabolomics GC/MS Data
Fragment-level analysis of gas chromatography-massspectrometry metabolomics data.
Authors:
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flagme.pdf |flagme.html✨
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-1.63.0(bioc 3.21)flagme-1.62.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialexpressionmassspectrometry
Last updated 2 months agofrom:7b496c7189. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 10 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 10 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 10 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 10 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 10 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 10 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 10 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 10 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 10 2024 |
Exports:addAMDISPeaksaddChromaTOFPeaksaddXCMSPeaksbetweenAlignmentcalcTimeDiffsclusterAlignmentcorPrtdistToLibdpdynRTexportSpectragatherInfoheadToTailPlotimportSpecimputePeaksmatchSpecmultipleAlignmentndpRTnormDotProductparseChromaTOFparseELUpeaksAlignmentpeaksDatasetplotAlignedFragsplotAlignmentplotChromplotClustAlignmentplotFragsplotImageprogressiveAlignmentretFatMatrixrmaFitUnitshow
Dependencies:abindaffyaffyioAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitopsbslibcachemCAMERAcaToolscheckmatecliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgcspikelitegenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgraphgridExtragtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmennetopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppreshape2Rhdf5librlangrmarkdownrpartrstudioapiS4ArraysS4VectorssassscalessnowSparseArraySparseMSpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc
\texttt{flagme}: Fragment-level analysis of \ GC-MS-based metabolomics data
Rendered fromflagme.Rnwusingutils::Sweaveon Dec 10 2024.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 Dec 10 2024.Last update: 2023-02-07
Started: 2021-10-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add AMDIS peak detection results | addAMDISPeaks |
| Add ChromaTOF peak detection results | addChromaTOFPeaks |
| addXCMSPeaks | addXCMSPeaks |
| Data Structure for "between" alignment of many GCMS samples | betweenAlignment betweenAlignment-class betweenAlignment-method betweenAlignment-show show, |
| Calculate retention time shifts from profile alignments | calcTimeDiffs |
| Data Structure for a collection of all pairwise alignments of GCMS runs | clusterAlignment clusterAlignment-class clusterAlignment-plot clusterAlignment-show plot,clusterAlignment,ANY-method plot,clusterAlignment-method show,clusterAlignment-method |
| Retention Time Penalized Correlation | corPrt |
| deDuper | deDuper |
| distToLib | distToLib |
| Dynamic programming algorithm, given a similarity matrix | dp |
| dynRT | dynRT |
| A class description | eitherMatrix-class |
| exportSpectra | exportSpectra |
| Gathers abundance informations from an alignment | gatherInfo |
| Head to tail plot | headToTailPlot |
| importSpec | importSpec |
| Imputatin of locations of peaks that were undetected | imputePeaks |
| matchSpec | matchSpec |
| Data Structure for multiple alignment of many GCMS samples | multipleAlignment multipleAlignment-class multipleAlignment-class, multipleAlignment-method multipleAlignment-show, |
| Retention Time Penalized Normalized Dot Product | ndpRT |
| Normalized Dot Product | normDotProduct |
| Parser for ChromaTOF files | parseChromaTOF |
| Parser for ELU files | parseELU |
| Data Structure for pairwise alignment of 2 GCMS samples | peaksAlignment 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 results | peaksDataset peaksDataset-class peaksDataset-plot peaksDataset-show plot,peaksDataset,ANY-method plot,peaksDataset-method show,peaksDataset-method |
| plotAlignedFrags | plotAlignedFrags |
| plotAlignment | plotAlignment,peaksAlignment-method |
| Plotting functions for GCMS data objects | plotChrom,peaksDataset-method |
| plotClustAlignment | plotClustAlignment,clusterAlignment-method |
| plotFrags | plotFrags |
| Plot of images of GCMS data | plotImage plotImage,peaksDataset-method |
| Data Structure for progressive alignment of many GCMS samples | progressiveAlignment progressiveAlignment-class progressiveAlignment-show show,progressiveAlignment-method |
| retFatMatrix | retFatMatrix |
| Fits a robust linear model (RLM) for one metabolite | rmaFitUnit |
| Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs | show,multipleAlignment-method |