Package: yamss 1.31.0

Leslie Myint

yamss: Tools for high-throughput metabolomics

Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis. At the core of these methods is a peak detection phase that pools information across all samples simultaneously. This is in contrast to other methods that detect peaks in a sample-by-sample basis.

Authors:Leslie Myint [cre, aut], Kasper Daniel Hansen [aut]

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yamss.pdf |yamss.html✨
yamss/json (API)
NEWS

# Install 'yamss' in R:

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

Bug tracker:https://github.com/hansenlab/yamss/issues

Datasets:

cmsRawExample - An example cmsRaw object

On BioConductor:yamss-1.31.0(bioc 3.20)yamss-1.30.0(bioc 3.19)

bioconductor-package

15 exports 1.00 score 68 dependencies 1 mentions

Last updated 2 months agofrom:7072a74158

Exports:bakedpi CMSslice colData densityCutoff densityEstimate densityQuantiles diffrep getEICS getTIC peakBounds peakQuants plotDensityRegion readMSdata show slicepi

Dependencies:abind askpass base64enc Biobase BiocGenerics bitops bslib cachem cli crayon curl data.table DelayedArray digest EBImage evaluate fastmap fftwtools fontawesome fs GenomeInfoDb GenomeInfoDbData GenomicRanges glue highr htmltools htmlwidgets httr IRanges jpeg jquerylib jsonlite knitr lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats memoise mime mzR ncdf4 openssl png ProtGenerics R6 rappdirs Rcpp RCurl Rhdf5lib rlang rmarkdown S4Arrays S4Vectors sass SparseArray statmod SummarizedExperiment sys tiff tinytex UCSC.utils xfun XVector yaml zlibbioc

The yamss User's Guide

Leslie Myint, Kasper Daniel Hansen

Rendered fromyamss.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-22
Started: 2016-10-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Process raw data to compute density estimate.	bakedpi
A class to hold chromatography-mass spectrometry preprocessing information.	CMSproc-class densityEstimate densityQuantiles show,CMSproc-method
A class to hold chromatography-mass spectrometry raw data and metadata.	CMSraw-class colData,CMSraw-method show,CMSraw-method
An example cmsRaw object	cmsRawExample
A class to hold chromatography-mass spectrometry peak bounds and quantifications.	CMSslice CMSslice-class densityCutoff peakBounds peakQuants show,CMSslice-method
Perform differential analysis.	diffrep
Compute extracted ion chromatograms for multiple regions.	getEICS
Compute total ion chromatogram (TIC) for a sample.	getTIC
Image plot of region of density estimate.	plotDensityRegion
Read raw mass spectral data files.	readMSdata
Process raw data to compute density estimate.	slicepi