MSstatsPTM

DOI: 10.18129/B9.bioc.MSstatsPTM  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MSstatsPTM.

Statistical Characterization of Post-translational Modifications

Bioconductor version: 3.17

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

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

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

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("MSstatsPTM")

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("MSstatsPTM")

 

HTML	R Script	MSstatsPTM LabelFree Workflow
HTML	R Script	MSstatsPTM TMT Workflow
PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version	2.2.4
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices, MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp, Biostrings, checkmate, ggrepel
LinkingTo	Rcpp
Suggests	knitr, rmarkdown, tinytest, covr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Vitek-Lab/MSstatsPTM/issues
Depends On Me
Imports Me	MSstatsLiP, MSstatsShiny
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MSstatsPTM_2.2.4.tar.gz
Windows Binary	MSstatsPTM_2.2.4.zip (64-bit only)
macOS Binary (x86_64)	MSstatsPTM_2.2.4.tgz
macOS Binary (arm64)	MSstatsPTM_2.2.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsPTM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsPTM
Bioc Package Browser	https://code.bioconductor.org/browse/MSstatsPTM/
Package Short Url	https://bioconductor.org/packages/MSstatsPTM/
Package Downloads Report	Download Stats