MSstatsTMT

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see MSstatsTMT.

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

Bioconductor version: 3.14

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 "4.1") 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")

MSstatsTMT User Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Proteomics, Software

Version 2.2.7

In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)

License Artistic-2.0

Depends R (>= 4.1)

Imports limma, lme4, lmerTest, methods, data.table, stats, utils, ggplot2, grDevices, graphics, MSstats, MSstatsConvert, checkmate

System Requirements

URL http://msstats.org/msstatstmt/

Bug Reports https://groups.google.com/forum/#!forum/msstats

Suggests BiocStyle, knitr, rmarkdown, testthat

Linking To

Enhances

Depends On Me

Imports Me MSstatsPTM, MSstatsTMTPTM

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_2.2.7.tar.gz

Windows Binary MSstatsTMT_2.2.7.zip

macOS 10.13 (High Sierra) MSstatsTMT_2.2.7.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 3.14 Source Archive