yamss: Tools for high-throughput metabolomics

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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.

Author
Leslie Myint [cre, aut], Kasper Daniel Hansen [aut]
Date of publication
None
Maintainer
Leslie Myint <lmyint1@jhu.edu>
License
Artistic-2.0
Version
1.0.1
URLs

View on Bioconductor

Man pages

bakedpi
Process raw data to compute density estimate.
CMSproc-class
A class to hold chromatography-mass spectrometry...
CMSraw-class
A class to hold chromatography-mass spectrometry raw data and...
CMSslice-class
A class to hold chromatography-mass spectrometry peak bounds...
diffrep
Perform differential analysis.
getEICS
Compute extracted ion chromatograms for multiple regions.
getTIC
Compute total ion chromatogram (TIC) for a sample.
plotDensityRegion
Image plot of region of density estimate.
slicepi
Process raw data to compute density estimate.

Files in this package

yamss/.travis.yml
yamss/DESCRIPTION
yamss/NAMESPACE
yamss/R
yamss/R/DataClasses.R
yamss/R/bakedpi.R
yamss/R/functions.R
yamss/R/reading.R
yamss/R/slicepi.R
yamss/R/utils.R
yamss/README.md
yamss/build
yamss/build/vignette.rds
yamss/data
yamss/data/cmsRawExample.rda
yamss/inst
yamss/inst/NEWS.Rd
yamss/inst/doc
yamss/inst/doc/yamss.R
yamss/inst/doc/yamss.Rmd
yamss/inst/doc/yamss.html
yamss/inst/scripts
yamss/inst/scripts/digests.rda
yamss/inst/scripts/makeCmsRawExample.R
yamss/inst/scripts/test_digest.R
yamss/inst/scripts/test_digest.Rout
yamss/man
yamss/man/CMSproc-class.Rd
yamss/man/CMSraw-class.Rd
yamss/man/CMSslice-class.Rd
yamss/man/bakedpi.Rd
yamss/man/cmsRawExample.rd
yamss/man/diffrep.Rd
yamss/man/getEICS.Rd
yamss/man/getTIC.Rd
yamss/man/plotDensityRegion.Rd
yamss/man/readMSdata.rd
yamss/man/slicepi.Rd
yamss/tests
yamss/tests/testthat
yamss/tests/testthat.R
yamss/tests/testthat/test-bakedpi.R
yamss/tests/testthat/test-read.R
yamss/vignettes
yamss/vignettes/framed.sty
yamss/vignettes/yamss.Rmd
yamss/vignettes/yamss.bib