multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.
Package details |
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Author | John Stansfield <stansfieldjc@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org> |
Bioconductor views | HiC Normalization Sequencing Software |
Maintainer | John Stansfield <stansfieldjc@vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org> |
License | MIT + file LICENSE |
Version | 1.13.0 |
URL | https://github.com/dozmorovlab/multiHiCcompare |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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