MSstats

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MSstats.

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


Bioconductor version: 3.12

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

Author: Meena Choi [aut, cre], Tsung-Heng Tsai [aut], Cyril Galitzine [aut], Ting Huang [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 "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MSstats")

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")
MSstats: Protein/Peptide significance analysis HTML R Script
Reference Manual PDF

Details

biocViews ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse
Version 3.22.1
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License Artistic-2.0
Depends R (>= 3.6)
Imports lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel, preprocessCore, reshape2, survival, statmod, minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow, foreach, data.table, MASS, dplyr, tidyr, broom, purrr, stringr
System Requirements
URL http://msstats.org
Bug Reports https://groups.google.com/forum/#!forum/msstats
See More
Suggests BiocStyle, knitr, rmarkdown, MSstatsBioData
Linking To
Enhances
Depends On Me
Imports Me artMS, MSstatsSampleSize, MSstatsTMT
Suggests Me MSstatsBioData, MSstatsTMTPTM
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSstats_3.22.1.tar.gz
Windows Binary MSstats_3.22.1.zip
macOS 10.13 (High Sierra) MSstats_3.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstats
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstats
Bioc Package Browser https://code.bioconductor.org/browse/MSstats/
Package Short Url https://bioconductor.org/packages/MSstats/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive