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isobar

Analysis and quantitation of isobarically tagged MSMS proteomics data


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews Bioinformatics, ImmunoOncology, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl, Software
Version 1.48.0
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
See More
Suggests MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS
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Package Archives

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

Source Package isobar_1.48.0.tar.gz
Windows Binary isobar_1.48.0.zip
macOS Binary (x86_64) isobar_1.48.0.tgz
macOS Binary (arm64) isobar_1.48.0.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