ChIPseeqer is a computational framework for the analysis of ChIP-seq datasets.

It includes quality control tools for the raw data and peak detection.

Moreover, it offers:

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

ChIPseeqer is open-source software, released under the GNU GENERAL PUBLIC LICENSE v.3. For more information, please see the file called LICENSE.

Annotation data are available at:

http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/

For installation instructions please take a look at the file called INSTALL.

ChIPseeqer is fully documented online at:

https://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml

The ChIPseeqer software has been developed in the Elemento lab, at the Institute of Computational Biology of Weill Cornell Medical College, by:

• Eugenia Giannopoulou, Ph.D. ([email protected])
• Olivier Elemento, Ph.D. ([email protected])

If you have any questions, bug reports or features suggestions please contact:

• Eugenia Giannopoulou, Ph.D. ([email protected])