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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 (3.20)

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")

# 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 2.13.1
In Bioconductor since BioC 3.8 (R-3.5) (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, plotly, htmltools
System Requirements
URL http://msstats.org/msstatstmt/
Bug Reports https://groups.google.com/forum/#!forum/msstats
See More
Suggests BiocStyle, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me MSstatsPTM, MSstatsShiny
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSstatsTMT_2.13.1.tar.gz
Windows Binary MSstatsTMT_2.13.0.zip
macOS Binary (x86_64) MSstatsTMT_2.13.1.tgz
macOS Binary (arm64) MSstatsTMT_2.13.0.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