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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