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Enables broad and analysis of ChIP-seq data. ChIPseeqer is a comprehensive computational framework that includes: (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, published ChIP-seq datasets), (5) conservation analysis, (6) clustering analysis, (7) visualization tools, (8) integration and comparison across different ChIP-seq experiments.

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ChIPseeqer classification

ChIPseeqer specifications

Software type:
Restrictions to use:
GNU General Public License version 3.0
Command line interface, Graphical user interface
Operating system:
Unix/Linux, Mac OS
Computer skills:

ChIPseeqer distribution


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ChIPseeqer support


  • Olivier Elemento <>

Additional information


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HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA

Funding source(s)

Supported by the CAREER grant from National Science Foundation (DB1054964), as well as by startup funds from the Institute for Computational Biomedicine, Weill Cornell Medical College.

Link to literature

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