Package: flagme 1.61.0

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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NEWS

# Install 'flagme' in R:

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

On BioConductor:flagme-1.61.0(bioc 3.20)flagme-1.60.0(bioc 3.19)

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

bioconductor-package

33 exports 1.24 score 158 dependencies 1 mentions

Last updated 2 months agofrom:05d260a3ce

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

Dependencies:abind affy affyio AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel bitops bslib cachem CAMERA caTools checkmate cli clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options gcspikelite generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment munsell mzID mzR ncdf4 nlme nnet openssl pcaMethods pillar pkgconfig plotly plyr preprocessCore prettyunits progress promises ProtGenerics PSMatch purrr QFeatures R6 rappdirs RBGL RColorBrewer Rcpp reshape2 Rhdf5lib rlang rmarkdown rpart rstudioapi S4Arrays S4Vectors sass scales snow SparseArray SparseM Spectra statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite vsn withr xcms xfun XML XVector yaml zlibbioc

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

Rendered fromflagme.Rnwusingutils::Sweaveon Jul 03 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 Jul 03 2024.

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

Citation

Development and contributors

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