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:
- 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
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])