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Table 3 Visualization tools for Hi-C data

From: Molecular and computational approaches to map regulatory elements in 3D chromatin structure

Software

How to run

Input

Interactivity

DNARchitect [228]

Web-based/R package

.bed, .bedpe, .bedgraph, or file with custom headers

Interactive

gcMapExplorer [229]

Linux command line to start GUI

.Gcmap, .ccmap, and .hdf5

Interactive

HiCorr [226]

Linux command line

Anchor-to-anchor looping pairs file from normalization

Non-interactive

HiCPlotter [191]

Python script

.bedgraph, and .matrix from HiC-Pro

Non-interactive

HiGlass [190]

Web-based/Linux command line/Python package

.cool, .mcool, .bigwig, .bedgraphs, and .bed-like

Interactive

HiTC [192]

R package

.matrix from HiC-Pro

Non-interactive

Juicebox [189]

Web-based/local installation on Linux/Windows/Mac

.hic

Interactive

UCSC Genome Browser [117]

Web-based

.hic

Interactive

WashU Epigenome Browser [121]

Web-based

.hic, .cool, .bigInteract, and .longrange

Interactive

3D Genome Browser [193]

Web-based

.butlr

Interactive