PSU 3D Genome Browser

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1519-9

Methods

linear single view single scale single focus segregated no abstraction no arrangement within interconnection between interconnection segment sparse type segment contiguous type point sparse type point contiguous type

Tool

Access Format web application
Supported Files other
License unavailable
Tool name

PSU 3D Genome Browser
Tool Link http://3dgenome.org
Documentation http://promoter.bx.psu.edu/hi-c/tutorial.html

Paper

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Wang Y, Song F, Zhang B, Zhang L, Xu J, Kuang D, et al. The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions. Genome Biol. genomebiology.biomedcentral.com; 2018;19: 151.

Abstract

Here, we introduce the 3D Genome Browser, http://3dgenome.org , which allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. We design a new binary data format for Hi-C data that reduces the file size by at least a magnitude and allows users to visualize chromatin interactions over millions of base pairs within seconds. Our browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure.