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 or Max OS X.
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.