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Bioinformatics. 2017 May 15;33(10):1570-1571. doi: 10.1093/bioinformatics/btx016.

annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.

Tang X1,2,3, Srivastava A1,2,3, Liu H1,2,3, Machiraju R4, Huang K5, Leone G1,2,3.

Author information

1
Department of Molecular Virology, Immunology and Medical Genetics College of Medicine, The Ohio State University, Columbus, OH, USA.
2
Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, OH, USA.
3
Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
4
Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
5
Computer Science and Engineering, The Ohio State University, Columbus, OH, USA.

Abstract

Summary:

We developed annoPeak, a web application to annotate, visualize and compare predicted protein-binding regions derived from ChIP-seq/ChIP-exo-seq experiments using human and mouse cells. Users can upload peak regions from multiple experiments onto the annoPeak server to annotate them with biological context, identify associated target genes and categorize binding sites with respect to gene structure. Users can also compare multiple binding profiles intuitively with the help of visualization tools and tables provided by annoPeak. In general, annoPeak will help users identify patterns of genome wide transcription factor binding profiles, assess binding profiles in different biological contexts and generate new hypotheses.

Availability and Implementation:

The web service is freely accessible through URL: http://ccc-annopeak.osumc.edu/annoPeak . Source code is available at https://github.com/XingTang2014/annoPeak .

Contact:

gustavo.leone@osumc.edu or kun.huang@osumc.edu.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28169395
PMCID:
PMC5860050
DOI:
10.1093/bioinformatics/btx016
[Indexed for MEDLINE]
Free PMC Article

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