MSstatsTMT

DOI: 10.18129/B9.bioc.MSstatsTMT  

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

Bioconductor version: Release (3.16)

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

Maintainer: Ting Huang <thuang0703 at gmail.com>

Installation

To install this package, start R (version "4.2") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MSstatsTMT")

 

HTML	R Script	MSstatsTMT User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Proteomics, Software
Version	2.6.1
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	http://msstats.org/msstatstmt/
BugReports	https://groups.google.com/forum/#!forum/msstats
Depends On Me
Imports Me	MSstatsPTM, MSstatsShiny
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSstatsTMT_2.6.1.tar.gz
Windows Binary	MSstatsTMT_2.6.1.zip
macOS Binary (x86_64)	MSstatsTMT_2.6.1.tgz
macOS Binary (arm64)	MSstatsTMT_2.6.1.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
Old Source Packages for BioC 3.16	Source Archive