ChIP-seq differential binding
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

Supplement

Releases

version 1.1.4

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.

version 1.1.6

Download. R 2.14 above compatible.

Features

  • 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 bound sites.

Installation instructions

  • 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 DBChIP_1.1.6.tar.gz

Tutorial

Link
Any questions: contact kliang AT stat.wisc.edu