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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MSstats")
AuthorMeena Choi [aut, cre], Cyril Galitzine [aut], Tsung-Heng Tsai [aut], Olga Vitek [aut]
Date of publicationNone
MaintainerMeena Choi <mnchoi67@gmail.com>
LicenseArtistic-2.0
Version3.6.0
http://msstats.org

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

Functions

dataProcess Man page
dataProcessPlots Man page
DDARawData Man page
DDARawData.Skyline Man page
designSampleSize Man page
designSampleSizePlots Man page
DIARawData Man page
groupComparison Man page
groupComparisonPlots Man page
linear_quantlim Man page
MaxQtoMSstatsFormat Man page
modelBasedQCPlots Man page
MSstats Man page
MSstats-package Man page
nonlinear_quantlim Man page
plot_quantlim Man page
ProgenesistoMSstatsFormat Man page
quantification Man page
SkylinetoMSstatsFormat Man page
SpectronauttoMSstatsFormat Man page
SpikeInDataLinear Man page
SpikeInDataNonLinear Man page
SRMRawData Man page
transformMSnSetToMSstats Man page
transformMSstatsToMSnSet Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.