isobar

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see isobar.

Analysis and quantitation of isobarically tagged MSMS proteomics data

Bioconductor version: 3.9

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>

Citation (from within R, enter citation("isobar")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")

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	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bioinformatics, ImmunoOncology, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl, Software
Version	1.30.0
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 years)
License	LGPL-2
Depends	R (>= 2.10.0), Biobase, stats, methods
Imports	distr, plyr, biomaRt, ggplot2
System Requirements
URL	https://github.com/fbreitwieser/isobar
Bug Reports	https://github.com/fbreitwieser/isobar/issues

Suggests	MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	RforProteomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	isobar_1.30.0.tar.gz
Windows Binary	isobar_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	isobar_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/isobar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/isobar
Bioc Package Browser	https://code.bioconductor.org/browse/isobar/
Package Short Url	https://bioconductor.org/packages/isobar/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.9	Source Archive