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MSstatsTMT

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

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

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
MSstatsTMT User Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software
Version 2.9.0
In Bioconductor since BioC 3.8 (R-3.5) (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
Linking To
Suggests BiocStyle, knitr, rmarkdown, testthat
System Requirements
Enhances
URL http://msstats.org/msstatstmt/
Bug Reports https://groups.google.com/forum/#!forum/msstats
See More
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_2.9.0.tar.gz
Windows Binary MSstatsTMT_2.9.0.zip (64-bit only)
macOS Binary (x86_64) MSstatsTMT_2.9.0.tgz
macOS Binary (arm64) MSstatsTMT_2.9.0.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