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ChIPseqR
ChIPseqR is an R package to identify protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well. It is available under the General Public License and comes with absolutely no warranty.
News
- 14 September 2009
- Initial release
- 2 November 2009
- ChIPseqR is now availabe as part of Bioconductor.
Download
To install the latest version of ChIPseqR ensure that you are using a recent version of R and execute the following two lines of code within an R session:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseqR")
The initial release version of ChIPseqR is still available here.
Instructions for the installation of R packages can be found on the R Project website for Unix, Windows and Mac OS X.Documentation
The package documentation is available as PDF and HTML.A tutorial introducing the main functions of ChIPseqR and demonstrating its use for locating nucleosome positions is available as PDF.
Data
Sequencing data from a simulated experiment of nucleosome positioning in Arabidopsis is available at three different levels of coverage:- Sequences
- of 3 million (203MB), 6 million (403MB) and 10 million (668MB) reads per run with three replicates each.
- True read positions
- of all reads (101MB) and corresponding names (75MB).
- Feature sequence
- The sequence of underlying features (0.8MB) can be used to reconstruct the nucleosome and read densities.