MSstats

This is the development version of MSstats; for the stable release version, see MSstats.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13

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

Bioconductor version: Development (3.24)

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

Author: Meena Choi [aut, cre], Mateusz Staniak [aut], Devon Kohler [aut], Tony Wu [aut], Deril Raju [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")):

Meena Choi, Mateusz Staniak, Devon Kohler, Tony Wu, Deril Raju, Tsung-Heng Tsai, Ting Huang, Olga Vitek. MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments. doi:10.18129/B9.bioc.MSstats, R package version 4.21.1, https://bioconductor.org/packages/MSstats.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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
MSstats: Metabolomics workflow with MZMine	HTML	R Script
MSstats+: Peak quality-weighted differential analysis	HTML	R Script
MSstats: End to End Workflow	HTML	R Script
Reference Manual	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Normalization, Proteomics, QualityControl, Software, TimeCourse
Version	4.21.1
In Bioconductor since	BioC 2.13 (R-3.0) (13 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	MSstatsConvert, data.table, checkmate, MASS, htmltools, limma, lme4, preprocessCore, survival, utils, Rcpp, ggplot2 (>= 3.4.0), ggrepel, gplots, plotly, marray, stats, grDevices, graphics, methods, statmod, parallel, rlang
System Requirements
URL	http://msstats.org
Bug Reports	https://groups.google.com/forum/#!forum/msstats

Suggests	BiocStyle, knitr, rmarkdown, tinytest, covr, markdown, mockery, kableExtra
Linking To	Rcpp, RcppArmadillo
Enhances
Depends On Me	MSstatsBioNet
Imports Me	artMS, MSstatsBig, MSstatsLiP, MSstatsPTM, MSstatsShiny, MSstatsTMT
Suggests Me	MSstatsResponse
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MSstats_4.21.1.tar.gz
Windows Binary (x86_64)	MSstats_4.21.1.zip
macOS Binary (big-sur-x86_64)	MSstats_4.21.1.tgz
macOS Binary (sonoma-arm64)	MSstats_4.21.1.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