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:
Gene-level annotation of peaks
Pathways enrichment analysis
Regulatory element analysis, using either a de novo approach, known or user-defined motifs
Nongenic peak annotation (repeats, CpG islands, duplications)
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, Max OS X or Windows/Cygwin.
Making full use of this framework does not require any programming skills or specialized computers knowledge.
To install the GUI version follow the instructions here.
To install the command-line version follow the instructions here.
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.