Table 1 Comparison of toolkit functionality
Hi-Browse | Juicebox | my5C | 3D genome browser | Epigenome browser | |
|---|---|---|---|---|---|
Hi-C visualization | |||||
Intrachromosomal heat map | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Interchromosomal heat map | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Circular plot | \(\checkmark \) | \(\checkmark \) | |||
Rotated local heat map | \(\checkmark \) | \(\checkmark \) | |||
Local arc track | \(\checkmark \) | \(\checkmark \) | |||
Locus-specific circular plot | \(\checkmark \) | ||||
Virtual 4C plot | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Multi-dataset visualizations | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |
Hi-C signal transformations | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Supplemental data visualization | |||||
Supplemental data visualization | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
2D heat map features | \(\checkmark \) | ||||
Continuous-valued tracks | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Genome browser interface | \(\checkmark \) | \(\checkmark \) | |||
Format for uploaded Hi-C data | |||||
Sparse tab-delimited | \(\checkmark \) | ||||
Dense tab-delimited | \(\checkmark \) | \(\checkmark \) | |||
Sparse binary | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Pre-loaded Hi-C data sets | |||||
Rao et al. 2014 | \(\checkmark \) | \(\checkmark \) | |||
Dixon et al. 2012 | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |
Lieberman-Aiden et al. 2009 | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Normalized versions | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Supplemental data sets | |||||
Annotations | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
ENCODE tracks | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Roadmap Epigenome tracks | \(\checkmark \) | ||||
Implementation | |||||
Free | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) |
Open source | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | ||
Local installation option | \(\checkmark \) | \(\checkmark \) | |||
Wiki | \(\checkmark \) | ||||
Browser interface | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | \(\checkmark \) | |
Java interface | \(\checkmark \) | ||||