isobar
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see isobar.
Analysis and quantitation of isobarically tagged MSMS proteomics data
Bioconductor version: 3.11
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("isobar")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| isobar for quantification of PTM datasets | R Script | |
| isobar package for iTRAQ and TMT protein quantification | R Script | |
| Usecases for isobar package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bioinformatics, ImmunoOncology, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl, Software |
| Version | 1.34.0 |
| 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 |
| 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_1.34.0.tar.gz |
| Windows Binary | isobar_1.34.0.zip |
| macOS 10.13 (High Sierra) | isobar_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/isobar |
| Source Repository (Developer Access) | git clone [email protected]: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 3.11 | Source Archive |