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The user guide, source and binary files are now hosted in github:
Data:
Arabidopsis thaliana (pre-process tutorial)
Citation:
Grob S, Schmid MW, Grossniklaus U. (2014) HiC Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Molecular Cell, 55(5): 678-693 [PubMed]