external link: https://github.com/vaquerizaslab/chess developed by Nick Machnik and Silvia Galan in the Vaquerizas Lab (https://www.vaquerizaslab.org/)
CHESS is a command line tool for the comparison and automatic feature extraction for chromatin contact data. Its main purpose is to quantify the structural similarity of regions of arbitrary size between two datasets, extract structural features from these regions and cluster across the data.
Typical usecases are the identification of structural differences between experimental condition, or the assessment of structural conservation of chromatin across evolutionary timescales, as it also allows for inter-species comparisons.
Galan S, Machnik N, Kruse K, Díaz N, Marti-Renom MA & Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nat Genet 52, 1247–1255 (2020). https://doi.org/10.1038/s41588-020-00712-y