MSstatsTMTPTM

DOI: 10.18129/B9.bioc.MSstatsTMTPTM    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 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: 3.14

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

BiocManager::install("MSstatsTMTPTM")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
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
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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