MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments
Version 3.8.0

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

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
Version3.8.0
URL http://msstats.org
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MSstats")

Getting started

Package overview
README.md
MSstats

Popular man pages

dataProcess: Data pre-processing and quality control of MS runs of raw...
MaxQtoMSstatsFormat: Generate MSstats required input format for MaxQuant output
MSstats-package: Tools for protein significance analysis in DDA,SRM and DIA...
nonlinear_quantlim: Calculation of the LOB and LOD with a nonlinear fit
quantification: Protein sample quantification or group quantification
SpikeInDataLinear: Example dataset from an MRM spike-in experiment with a linear...
transformMSstatsToMSnSet: Transformation input format for MSstats to MSnSet class
See all...

All man pages Function index File listing

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

DDARawData Man page
DDARawData.Skyline Man page
DIARawData Man page
MSstats Man page
MSstats-package Man page
MaxQtoMSstatsFormat Man page Source code
ProgenesistoMSstatsFormat Man page Source code
SRMRawData Man page
SkylinetoMSstatsFormat Man page Source code
SpectronauttoMSstatsFormat Man page Source code
SpikeInDataLinear Man page
SpikeInDataNonLinear Man page
bilinear Source code
bilinear_LOD Source code
bilinear_LOD_nonlin Source code
cast_maxquant_to_wide_glf Source code
cast_maxquant_to_wide_silac Source code
chechGroupComparisonAgreement Source code
checkMissFeature Source code
checkMissGroupByFeature Source code
checkMissRunByFeature Source code
checkRepeated Source code
checkRunbyFeature Source code
checkSingleFeature Source code
checkSingleSubject Source code
checkTechReplicate Source code
checkUnequalSubject Source code
count.missing.percentage Source code
countMultiRun Source code
dataProcess Man page Source code
dataProcessPlots Man page Source code
designSampleSize Man page Source code
designSampleSizePlots Man page Source code
estimableFixedQuantification Source code
estimableFixedQuantificationSurvival Source code
estimableFixedRandom Source code
estimableRandomQuantification Source code
fit.model.single Source code
fit.quantification.run Source code
fun_error Source code
getParameterFixed Source code
getParameterRandom Source code
ggplotColours Source code
groupComparison Man page Source code
groupComparisonPlots Man page Source code
linear Source code
linear_quantlim Man page Source code
make.contrast.based Source code
make.contrast.free Source code
make.contrast.free.single Source code
make.contrast.group.quantification Source code
make.contrast.group.quantification.reference Source code
make.contrast.run.quantification Source code
make.contrast.run.quantification.Survival Source code
make.contrast.run.quantification.reference Source code
make.contrast.subject.quantification Source code
make.contrast.subject.quantification.reference Source code
make.contrast.subject.quantification.single Source code
melt_maxquant_to_long_glf Source code
melt_maxquant_to_long_silac Source code
modelBasedQCPlots Man page Source code Source code
multiplot Source code
nonlinear_quantlim Man page Source code
nvlinear Source code
plot_quantlim Man page Source code
quantification Man page Source code
remove_feature_with_few Source code
remove_feature_with_few_progenesis Source code
runQuantification Source code
second Source code
ter.wls.fit.model Source code
theme_complete_bw Source code
transformMSnSetToMSstats Man page Source code
transformMSstatsToMSnSet Man page Source code
ttest.logsum Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/DataProcess.R
R/DataProcessPlots.R
R/GroupComparison.R
R/GroupComparisonPlots.R
R/MaxQtoMSstatsFormat.R
R/ProgenesistoMSstatsFormat.R
R/Quantification.R
R/SampleSizeCalculation.R
R/SkylinetoMSstatsFormat.R
R/SpectronauttoMSstatsFormat.R
R/TransformMSnSet.R
R/linear_quantlim.R
R/lodq_util.R
R/methods.R
R/modelBasedQCPlots.R
R/nonlinear_quantlim.R
R/plot_quantlim.R
README.md
build
build/vignette.rds
data
data/DDARawData.RData
data/DDARawData.Skyline.RData
data/DIARawData.RData
data/SRMRawData.RData
data/SpikeInDataLinear.RData
data/SpikeInDataNonLinear.RData
inst
inst/CITATION
inst/doc
inst/doc/MSstats-manual.pdf
inst/doc/MSstats.R
inst/doc/MSstats.Rmd
inst/doc/MSstats.html
man
man/DDARawData.Rd
man/DDARawData.Skyline.Rd
man/DIARawData.Rd
man/MSstats-package.Rd
man/MaxQtoMSstatsFormat.Rd
man/ProgenesistoMSstatsFormat.Rd
man/SRMRawData.Rd
man/SkylinetoMSstatsFormat.Rd
man/SpectronauttoMSstatsFormat.Rd
man/SpikeInDataLinear.Rd
man/SpikeInDataNonLinear.Rd
man/dataProcess.Rd
man/dataProcessPlots.Rd
man/designSampleSize.Rd
man/designSampleSizePlots.Rd
man/groupComparison.Rd
man/groupComparisonPlots.Rd
man/linear_quantlim.Rd
man/modelBasedQCPlots.Rd
man/nonlinear_quantlim.Rd
man/plot_quantlim.Rd
man/quantification.Rd
man/transformMSnSetToMSstats.Rd
man/transformMSstatsToMSnSet.Rd
vignettes
vignettes/MSstats.Rmd
MSstats documentation built on May 20, 2017, 10:11 p.m.

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