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

DOI: 10.18129/B9.bioc.MSstats

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>

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

Installation

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse

Version 4.0.1

In Bioconductor since BioC 2.13 (R-3.0) (10.5 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

System Requirements

URL http://msstats.org

Bug Reports https://groups.google.com/forum/#!forum/msstats

Suggests BiocStyle, knitr, rmarkdown, MSstatsBioData, tinytest, covr, markdown

Linking To Rcpp, RcppArmadillo

Enhances

Depends On Me

Imports Me artMS, MSstatsPTM, 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_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

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 3.13 Source Archive