iTagPlot: an accurate computation and interactive drawing tool for tag density plot

Sung-Hwan Kim; Onyeka Ezenwoye; Hwan-Gue Cho; Keith D Robertson; Jeong-Hyeon Choi

doi:10.1093/bioinformatics/btv166

iTagPlot: an accurate computation and interactive drawing tool for tag density plot

Bioinformatics. 2015 Jul 15;31(14):2384-7. doi: 10.1093/bioinformatics/btv166. Epub 2015 Mar 19.

Authors

Sung-Hwan Kim¹, Onyeka Ezenwoye², Hwan-Gue Cho¹, Keith D Robertson³, Jeong-Hyeon Choi⁴

Affiliations

¹ School of Computer Science and Engineering, Pusan National University, Busan, South Korea.
² Hull College of Business, Georgia Regents University, Augusta, GA, USA.
³ Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
⁴ Cancer Center and Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA.

Abstract

Motivation: Tag density plots are very important to intuitively reveal biological phenomena from capture-based sequencing data by visualizing the normalized read depth in a region.

Results: We have developed iTagPlot to compute tag density across functional features in parallel using multicores and a grid engine and to interactively explore it in a graphical user interface. It allows us to stratify features by defining groups based on biological function and measurement, summary statistics and unsupervised clustering.

Availability and implementation: http://sourceforge.net/projects/itagplot/.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cell Line
Cluster Analysis
Computer Graphics
CpG Islands
DNA Methylation
Gene Expression
High-Throughput Nucleotide Sequencing
Humans
Sequence Tagged Sites*
Software*

Abstract

Publication types

MeSH terms

Grants and funding