HiCcompare

DOI: 10.18129/B9.bioc.HiCcompare    

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

Bioconductor version: Release (3.6)

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 permutation method for detecting differences between Hi-C datasets.

Author: John Stansfield [aut, cre], Mikhail Dozmorov [aut]

Maintainer: John Stansfield <stansfieldjc at vcu.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("HiCcompare")

Documentation

HTML	R Script	HiCcompare Usage Vignette
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.0.0
License	MIT + file LICENSE
Depends	R (>= 3.4.0), dplyr
Imports	data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools
LinkingTo
Suggests	knitr, rmarkdown, testthat
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	HiCcompare_1.0.0.tar.gz
Windows Binary	HiCcompare_1.0.0.zip
Mac OS X 10.11 (El Capitan)	HiCcompare_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiCcompare
Package Short Url	http://bioconductor.org/packages/HiCcompare/
Package Downloads Report	Download Stats