MSstats

DOI: 10.18129/B9.bioc.MSstats    

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

Bioconductor version: Release (3.8)

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

Author: Meena Choi [aut, cre], Cyril Galitzine [aut], Ting Huang [aut], Tsung-Heng Tsai [aut], Olga Vitek [aut]

Maintainer: Meena Choi <mnchoi67 at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MSstats", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("MSstats")

 

HTML R Script MSstats: Protein/Peptide significance analysis
PDF   Reference Manual
Text   NEWS

Details

biocViews MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse
Version 3.14.0
In Bioconductor since BioC 2.13 (R-3.0) (5 years)
License Artistic-2.0
Depends R (>= 3.4)
Imports lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel, preprocessCore, reshape2, survival, minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, stringr, randomForest
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, MSstatsBioData
SystemRequirements
Enhances
URL http://msstats.org
BugReports https://groups.google.com/forum/#!forum/msstats
Depends On Me
Imports Me artMS, MSstatsTMT
Suggests Me MSstatsBioData
Links To Me
Build Report  

Package Archives

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

Source Package MSstats_3.14.0.tar.gz
Windows Binary MSstats_3.14.0.zip
Mac OS X 10.11 (El Capitan) MSstats_3.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstats
Package Short Url http://bioconductor.org/packages/MSstats/
Package Downloads Report Download Stats

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