MSstatsTMTPTM

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

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

Installation

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


if (!require("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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version 1.1.2
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2, grDevices, graphics, MSstatsTMT, Rcpp
System Requirements
URL
Bug Reports https://github.com/Vitek-Lab/MSstatsTMTPTM/issues
See More
Suggests BiocStyle, knitr, rmarkdown, testthat, MSstats, covr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/MSstatsTMTPTM/
Package Short Url https://bioconductor.org/packages/MSstatsTMTPTM/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive