dozmorovlab/HiCdiff: HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

HiCdiff provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCdiff operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCdiff is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCdiff` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCdiff` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCdiff` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.

install.packages("remotes")
remotes::install_github("dozmorovlab/HiCdiff")