To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("MSstats")

In most cases, you don't need to download the package archive at all.

MSstats

Protein Significance Analysis in LC-MS, SRM and DIA for Label-free or Label-based Proteomics Experiments

Bioconductor version: 2.13

A set of tools for protein significance analysis in label-free or LC-MS, SRM and DIA experiments.

Author: Meena Choi <choi67 at purdue.edu>, Ching-Yun Chang <chang54 at purdue.edu>, Olga Vitek <ovitek at purdue.edu>

Maintainer: Meena Choi <choi67 at purdue.edu>

Citation (from within R, enter citation("MSstats")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("MSstats")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MSstats")

 

PDF Comparison1.pdf
PDF Comparison2.pdf
PDF Condition1.pdf
PDF Condition2.pdf
PDF DIA_constant_QQPlot4.pdf
PDF DIA_constant_ResidualPlot4.pdf
PDF DIA_ProfilePlot_269.pdf
PDF DIA_ProfilePlot_377.pdf
PDF Heatmap45Yeast1.pdf
PDF Heatmap45Yeast2.pdf
PDF LCMS_constant_ResidualPlot.pdf
PDF LCMS_Heatmap.pdf
PDF LCMS_ProfilePlot.pdf
PDF MSstatsOverview.pdf
PDF power.pdf
PDF ProfilePlot1.pdf
PDF ProfilePlot2.pdf
PDF R Script Protein quantification in LC-MS, SRM, DIA experiments
PDF QCPlot_all.pdf
PDF QCPlot_all_before.pdf
PDF QQPlot2.pdf
PDF ResidualPlot2.pdf
PDF SampleSizeReplicateYeast.pdf
PDF SRM_QQPlot_perFeature_heavy.pdf
PDF SRM_QQPlot_perFeature_light.pdf
PDF Volcano45Yeast1.pdf
PDF Volcano45Yeast2.pdf
PDF VolcanoYeast1.pdf
PDF VolcanoYeast2.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews Software
Version 2.0.1
In Bioconductor since BioC 2.13 (R-3.0)
License Artistic-2.0
Depends R (>= 3.0), Rcpp, MSnbase
Imports lme4, marray, limma, gplots, ggplot2
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source MSstats_2.0.1.tar.gz
Windows Binary MSstats_2.0.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) MSstats_2.0.1.tgz
Browse/checkout source (username/password: readonly)
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