isobar

DOI: 10.18129/B9.bioc.isobar    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see isobar.

Analysis and quantitation of isobarically tagged MSMS proteomics data

Bioconductor version: 3.8

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Author: Florian P Breitwieser <florian.bw at gmail.com> and Jacques Colinge <jacques.colinge at inserm.fr>, with contributions from Alexey Stukalov <stukalov at biochem.mpg.de>, Xavier Robin <xavier.robin at unige.ch> and Florent Gluck <florent.gluck at unige.ch>

Maintainer: Florian P Breitwieser <florian.bw at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("isobar")

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("isobar")

 

PDF	R Script	isobar for developers
PDF	R Script	isobar for quantification of PTM datasets
PDF	R Script	isobar package for iTRAQ and TMT protein quantification
PDF	R Script	Usecases for isobar package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, ImmunoOncology, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl, Software
Version	1.28.1
In Bioconductor since	BioC 2.9 (R-2.14) (7.5 years)
License	LGPL-2
Depends	R (>= 2.10.0), Biobase, stats, methods
Imports	distr, plyr, biomaRt, ggplot2
LinkingTo
Suggests	MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS
SystemRequirements
Enhances
URL	https://github.com/fbreitwieser/isobar
BugReports	https://github.com/fbreitwieser/isobar/issues
Depends On Me
Imports Me
Suggests Me	RforProteomics
Links To Me
Build Report

Package Archives

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

Source Package	isobar_1.28.1.tar.gz
Windows Binary	isobar_1.28.1.zip
Mac OS X 10.11 (El Capitan)	isobar_1.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/isobar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/isobar
Package Short Url	http://bioconductor.org/packages/isobar/
Package Downloads Report	Download Stats