ChIPsim
ChIPsim is an R package for the simulation of ChIP-seq data. It is available under the General Public License and comes with absolutely no warranty.
News
- 2 November 2009 – Bioconductor 2.5 has been released. It includes the latest version of ChIPsim.
- 13 September 2009 – ChIPsim is now available as part of Bioconductor.
- 6 September 2009 – Improvements to documentation.
- 30 August 2009 – Minor update to fix specification of imported packages.
- 28 July 2009 – Initial release
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("ChIPsim")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.
A tutorial introducing the main functions of ChIPsim and demonstrating its use for the simulation of a nucleosome positioning experiment is available as PDF. This document also includes a discussion of how to extend ChIPsim for use with different types of experiments.
Data
Sequencing data from a simulated ChIP-seq experiment of nucleosome positioning in Arabidopsis is available (read sequences, fastq file, 223 MB; read positions, text file, 70 MB and underlying feature sequence, R data file). The TAIR 8 assembly of the Arabidopsis genome was used to generate read sequences.
Contact
For questions, comments and bug reports please contact Peter Humburg.