MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

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A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.

Author
Meena Choi [aut, cre], Cyril Galitzine [aut], Tsung-Heng Tsai [aut], Olga Vitek [aut]
Date of publication
None
Maintainer
Meena Choi <mnchoi67@gmail.com>
License
Artistic-2.0
Version
3.6.0
URLs

View on Bioconductor

Man pages

dataProcess
Data pre-processing and quality control of MS runs of raw...
dataProcessPlots
Visualization for explanatory data analysis
DDARawData
Example dataset from a label-free DDA, a controlled spike-in...
DDARawData.Skyline
Example dataset from a label-free DDA, a controlled spike-in...
designSampleSize
Planning future experimental designs of Selected Reaction...
designSampleSizePlots
Visualization for sample size calculation
DIARawData
Example dataset from a label-free DIA, a group comparison...
groupComparison
Finding differentially abundant proteins across conditions in...
groupComparisonPlots
Visualization for model-based analysis and summarizing...
linear_quantlim
Calculation of the LOB and LOD with a linear fit
MaxQtoMSstatsFormat
Generate MSstats required input format for MaxQuant output
modelBasedQCPlots
Visualization for model-based quality control in fitting...
MSstats-package
Tools for protein significance analysis in DDA,SRM and DIA...
nonlinear_quantlim
Calculation of the LOB and LOD with a nonlinear fit
plot_quantlim
Plot of the curve used to calculate LOB and LOD
ProgenesistoMSstatsFormat
Generate MSstats required input format for Progenesis output
quantification
Protein sample quantification or group quantification
SkylinetoMSstatsFormat
Generate MSstats required input format for Skyline output
SpectronauttoMSstatsFormat
Generate MSstats required input format for Spectronaut output
SpikeInDataLinear
Example dataset from an MRM spike-in experiment with a linear...
SpikeInDataNonLinear
Example dataset from an MRM spike-in experiment with a...
SRMRawData
Example dataset from a SRM experiment with stable isotope...
transformMSnSetToMSstats
Transforms a MSnSet class dataset into a required input for...
transformMSstatsToMSnSet
Transformation input format for MSstats to MSnSet class

Files in this package

MSstats/.BBSoptions
MSstats/DESCRIPTION
MSstats/NAMESPACE
MSstats/NEWS
MSstats/R
MSstats/R/DataProcess.R
MSstats/R/DataProcessPlots.R
MSstats/R/GroupComparison.R
MSstats/R/GroupComparisonPlots.R
MSstats/R/MaxQtoMSstatsFormat.R
MSstats/R/ProgenesistoMSstatsFormat.R
MSstats/R/Quantification.R
MSstats/R/SampleSizeCalculation.R
MSstats/R/SkylinetoMSstatsFormat.R
MSstats/R/SpectronauttoMSstatsFormat.R
MSstats/R/TransformMSnSet.R
MSstats/R/linear_quantlim.R
MSstats/R/lodq_util.R
MSstats/R/methods.R
MSstats/R/modelBasedQCPlots.R
MSstats/R/nonlinear_quantlim.R
MSstats/R/plot_quantlim.R
MSstats/README.md
MSstats/build
MSstats/build/vignette.rds
MSstats/data
MSstats/data/DDARawData.RData
MSstats/data/DDARawData.Skyline.RData
MSstats/data/DIARawData.RData
MSstats/data/SRMRawData.RData
MSstats/data/SpikeInDataLinear.RData
MSstats/data/SpikeInDataNonLinear.RData
MSstats/inst
MSstats/inst/CITATION
MSstats/inst/doc
MSstats/inst/doc/MSstats-manual.pdf
MSstats/inst/doc/MSstats.R
MSstats/inst/doc/MSstats.Rmd
MSstats/inst/doc/MSstats.html
MSstats/man
MSstats/man/DDARawData.Rd
MSstats/man/DDARawData.Skyline.Rd
MSstats/man/DIARawData.Rd
MSstats/man/MSstats-package.Rd
MSstats/man/MaxQtoMSstatsFormat.Rd
MSstats/man/ProgenesistoMSstatsFormat.Rd
MSstats/man/SRMRawData.Rd
MSstats/man/SkylinetoMSstatsFormat.Rd
MSstats/man/SpectronauttoMSstatsFormat.Rd
MSstats/man/SpikeInDataLinear.Rd
MSstats/man/SpikeInDataNonLinear.Rd
MSstats/man/dataProcess.Rd
MSstats/man/dataProcessPlots.Rd
MSstats/man/designSampleSize.Rd
MSstats/man/designSampleSizePlots.Rd
MSstats/man/groupComparison.Rd
MSstats/man/groupComparisonPlots.Rd
MSstats/man/linear_quantlim.Rd
MSstats/man/modelBasedQCPlots.Rd
MSstats/man/nonlinear_quantlim.Rd
MSstats/man/plot_quantlim.Rd
MSstats/man/quantification.Rd
MSstats/man/transformMSnSetToMSstats.Rd
MSstats/man/transformMSstatsToMSnSet.Rd
MSstats/vignettes
MSstats/vignettes/MSstats.Rmd