Table 1.

Processing software for 3C-type of data

Software	Authors	Description
r3Cseq	Thongjuea et al., 2013 [129]	R package. It uses BAM alignment files as input, and performs aligned reads counting, read count normalization, statistical analysis of interactions and data visualization or data export of contacting regions
HiTC	Servant, 2012 [130]	R package. It allows the use of both 5C and Hi-C data and offers quality control, normalization and visualization of heatmaps
fourSig	Williams, 2014 [131]	R package. Includes fragment filtering options
Basic4Cseq	Walter, 2014 [132]	R package. Also includes fragment filtering options, and provides more sophisticated visualization options
My5C	Lajoie, 2009 [108]	(http://my5c.umassmed.edu/welcome/welcome.php)
HOMER suite	Heinz, 2010 [133]	(http://homer.salk.edu/homer/interactions/index.html)
Hi-Browse	Paulsen, 2014 [134]	(https://hyperbrowser.uio.no/3d/)