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>

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

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
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
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/
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