ChIPseeqer
A comprehensive framework for the analysis of ChIP-seq data
Description
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:
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Peak detection
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)
Conservation analysis
Clustering analysis
Visualization
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.
Availability
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.
Tutorial
Comprehensive tutorials on how to use the provided computational tools to analyze ChIP-seq data are available for ChIPseeqer GUI and command-line.
Citation
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.
Contact
For questions, comments and suggestions please contact Jenny Giannopoulou.