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 |