NEW: The ChIPseeqer paper is out and highlighted as


A comprehensive framework for the analysis of ChIP-seq data


ChIPseeqer, is an integrative and comprehensive framework that allows the users to perform in-depth analysis of ChIP-seq datasets through easily customized workflows.
ChIPseeqer offers an efficient and user-friendly suite of computational tools that assist in analyzing and exploring a dataset from multiple perspectives.
The framework includes:

  1. Peak detection
  2. Gene-level annotation of peaks
  3. Pathways enrichment analysis
  4. Regulatory element analysis, using either a de novo approach, known or user-defined motifs
  5. Nongenic peak annotation (repeats, CpG islands, duplications)
  6. Conservation analysis
  7. Clustering analysis
  8. Visualization
  9. Integration and comparison across different ChIP-seq experiments

The framework is freely available as a command-line set of programs but also as a user-friendly GUI application.
It is designed to run on a standard desktop or laptop running Linux or Max OS X.
Making full use of this framework does not require any programming skills or specialized computers knowledge.


Download ChIPseeqer-2.0

Installation Instructions

To install the GUI version follow the instructions here.

To install the command-line version follow the instructions here.


Comprehensive tutorials on how to use the provided computational tools to analyze ChIP-seq data are available for ChIPseeqer GUI and command-line.


If you use ChIPseeqer in your research, please cite the following paper:

An integrated ChIP-seq analysis platform with customizable workflows, Eugenia G Giannopoulou and Olivier Elemento, BMC Bioinformatics 2011, 12:277.


For questions, comments and suggestions please contact Jenny Giannopoulou.

Elemento lab, June 2011