DiffTAD: Detecting Differential contact frequency in Topologically Associating Domains Hi-C experiments between conditions

MotivationIn recent years, the interest in analyzing chromosome conformation by Hi-C and related techniques has grown. It has been shown that contact frequency matrices obtained by these methods correlate with other methods of measurement of activity such as transcriptomics and histone modification assays. This brings a question of testing for differential contact frequency between experiments to the field.\n\nResultsIn this work, we provide a freely available software that implements two statistical methods for testing the significance of differential contact frequency in topological domains between two experiments. One method follows an empirical, permutation based approach to computing p-values, while the other is a parametric test based on the Poisson-Binomial distribution.\n\nAvailabilityThe software is freely available on the GNU General Public License at https://bitbucket.org/rzaborowski/differential-analysis\n\nContact[r.zaborowski|bartek]@mimuw.edu.pl\n\nSupplementary informationSupplementary data are available at Bioinformatics online.