To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("isobar")
In most cases, you don't need to download the package archive at all.
isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data
Bioconductor version: 3.0
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 <fbreitwieser at cemm.oeaw.ac.at> and Jacques Colinge <jcolinge at cemm.oeaw.ac.at>, with contributions from Xavier Robin <xavier.robin at unige.ch> and Florent Gluck <florent.gluck at unige.ch>
Maintainer: Florian P Breitwieser <fbreitwieser at cemm.oeaw.ac.at>
Citation (from within R,
enter citation("isobar")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("isobar")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("isobar")
| R Script | isobar for developers | |
| R Script | isobar for quantification of PTM datasets | |
| R Script | isobar package for iTRAQ and TMT protein quantification | |
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | Bioinformatics, MassSpectrometry, MultipleComparisons, Proteomics, QualityControl, Software |
| Version | 1.12.2 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | LGPL-2 |
| Depends | R (>= 2.10.0), Biobase, stats, methods, plyr |
| Imports | distr |
| LinkingTo | |
| Suggests | MSnbase, OrgMassSpecR, XML, biomaRt, ggplot2, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, distr, DBI, MASS |
| SystemRequirements | |
| Enhances | |
| URL | http://www.ms-isobar.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | RforProteomics |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | isobar_1.12.2.tar.gz |
| Windows Binary | isobar_1.12.2.zip |
| Mac OS X 10.6 (Snow Leopard) | isobar_1.12.2.tgz |
| Mac OS X 10.9 (Mavericks) | isobar_1.12.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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