MSstatsTMTPTM

DOI: 10.18129/B9.bioc.MSstatsTMTPTM    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSstatsTMTPTM.

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Bioconductor version: 3.13

Tools for Post Translational Modification (PTM) and protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. The functions in this package should be used after PTM/protein summarization. They can be used to both plot the summarized results and model the summarized datasets.

Author: Devon Kohler [aut, cre], Ting Huang [aut], Mateusz Staniak [aut], Meena Choi [aut], Tsung-Heng Tsai [aut], Olga Vitek [aut]

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

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("MSstatsTMTPTM")

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("MSstatsTMTPTM")

 

HTML	R Script	MSstatsTMTPTM : A package for post translational modification (PTM) significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
HTML	R Script	MSstatsTMTPTM.Workflow.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version	1.1.2
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2, grDevices, graphics, MSstatsTMT, Rcpp
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, testthat, MSstats, covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Vitek-Lab/MSstatsTMTPTM/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSstatsTMTPTM_1.1.2.tar.gz
Windows Binary	MSstatsTMTPTM_1.1.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	MSstatsTMTPTM_1.1.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsTMTPTM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsTMTPTM
Package Short Url	https://bioconductor.org/packages/MSstatsTMTPTM/
Package Downloads Report	Download Stats