This page last changed on April 19, 2012 by Kun Liang.
The page provides download links to an R package for detection of differential binding with ChIP-seq data. The method is described in:
Liang, K. and Keles, S. (2012), "Detecting differential binding of transcription factors with ChIP-seq", Bioinformatics, 28, 121-122, doi: 10.1093/bioinformatics/btr605
Download. R 2.12 and 2.13 compatible. Adaptive FDR control option available. Default is set to no subtraction of input when counting binding reads.
Download. R 2.14 above compatible.
- Combine peak list from multiple conditions to consensus binding sites.
- Count reads around consensus binding sites.
- Testing for differential binding.
- Produce coverage plot for differentially
- First, install edgeR and DESeq from Bioconductor.
- Within R: install.packages("path/DBChIP_1.1.6.tar.gz",
repo=NULL, type="source", dependencies = TRUE), where path is the path to the package.
- Outside R: R CMD INSTALL