MSstatsTMTPTM

DOI: 10.18129/B9.bioc.MSstatsTMTPTM    

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

Bioconductor version: Release (3.12)

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 "4.0") 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 1.0.1
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License Artistic-2.0
Depends R (>= 4.0)
Imports dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2, grDevices, graphics, MSstatsTMT
LinkingTo
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_1.0.1.tar.gz
Windows Binary MSstatsTMTPTM_1.0.1.zip
macOS 10.13 (High Sierra) MSstatsTMTPTM_1.0.1.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
Old Source Packages for BioC 3.12 Source Archive

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