HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare 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. HiCcompare 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.`HiCcompare` 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, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

Package details

AuthorJohn Stansfield <stansfieldjc@vcu.edu>, Kellen Cresswell <cresswellkg@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
Bioconductor views HiC Normalization Sequencing Software
MaintainerJohn Stansfield <stansfieldjc@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
LicenseMIT + file LICENSE
URL https://github.com/dozmorovlab/HiCcompare
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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HiCcompare documentation built on Nov. 8, 2020, 8:26 p.m.