This is the development version of HiCcompare; for the stable release version, see HiCcompare.
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasetsBioconductor version: Development (3.22)
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.
Author: Mikhail Dozmorov [aut, cre] ORCID: 0000-0002-0086-8358 , Kellen Cresswell [aut], John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
Citation (from within R, entercitation("HiCcompare")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("HiCcompare")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HiCcompare")Follow Installation instructions to use this package in your R session.
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