MSstatsTMT

Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Bioconductor version: Release (3.20)

The package provides statistical tools for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It provides multiple functionalities, including aata visualization, protein quantification and normalization, and statistical modeling and inference. Furthermore, it is inter-operable with other data processing tools, such as Proteome Discoverer, MaxQuant, OpenMS and SpectroMine.

Author: Devon Kohler [aut, cre], Ting Huang [aut], Meena Choi [aut], Mateusz Staniak [aut], Sicheng Hao [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at northeastern.edu>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("MSstatsTMT")

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

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	2.13.1
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate, plotly, htmltools
System Requirements
URL	http://msstats.org/msstatstmt/
Bug Reports	https://groups.google.com/forum/#!forum/msstats

Suggests	BiocStyle, knitr, rmarkdown, testthat
Linking To
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)	MSstatsTMT_2.13.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsTMT
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsTMT
Bioc Package Browser	https://code.bioconductor.org/browse/MSstatsTMT/
Package Short Url	https://bioconductor.org/packages/MSstatsTMT/
Package Downloads Report	Download Stats