MSstats

DOI: 10.18129/B9.bioc.MSstats    

This package is for version 3.13 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: 3.13

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

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

Maintainer: Meena Choi <mnchoi67 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse
Version	4.0.1
In Bioconductor since	BioC 2.13 (R-3.0) (8 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	MSstatsConvert, data.table, checkmate, MASS, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel, gplots, marray, stats, grDevices, graphics, methods
LinkingTo	Rcpp, RcppArmadillo
Suggests	BiocStyle, knitr, rmarkdown, MSstatsBioData, tinytest, covr, markdown
SystemRequirements
Enhances
URL	http://msstats.org
BugReports	https://groups.google.com/forum/#!forum/msstats
Depends On Me
Imports Me	artMS, MSstatsPTM, MSstatsSampleSize, MSstatsTMT
Suggests Me	MSstatsBioData, MSstatsTMTPTM
Links To Me
Build Report

Package Archives

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

Source Package	MSstats_4.0.1.tar.gz
Windows Binary	MSstats_4.0.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	MSstats_4.0.1.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	https://bioconductor.org/packages/MSstats/
Package Downloads Report	Download Stats