multiHiCcompare: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

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

AuthorJohn Stansfield [aut, cre], Mikhail Dozmorov [aut]
Bioconductor views HiC Normalization Sequencing Software
MaintainerJohn Stansfield <[email protected]>
LicenseMIT + file LICENSE
Version1.0.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("multiHiCcompare")

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multiHiCcompare documentation built on Nov. 1, 2018, 2:59 a.m.