High-throughput chromosome conformation capture data analysis software tools

Hi-C allows unbiased identification of chromatin interactions across an entire genome. Briefly: cells are crosslinked with formaldehyde; DNA is digested with a restriction enzyme that leaves a 5′-overhang; the 5′-overhang is filled, including a biotinylated residue; and the resulting blunt-end fragments are ligated under dilute conditions that favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of fragments that were originally in close spatial proximity in the nucleus.

Source text:
(Lieberman-Aiden et al., 2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science.

Data preprocessing

Data processing

Quantification

Data analysis

Annotation

Data visualization

Classification/Clustering

Network analysis

Integrative analysis

Workflows

Utilities

Unclassified tools