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.

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

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

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

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