HiCcompare

DOI: 10.18129/B9.bioc.HiCcompare    

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

Bioconductor version: Release (3.15)

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: John Stansfield <stansfieldjc at vcu.edu>, Kellen Cresswell <cresswellkg at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HiCcompare")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HiCcompare")

 

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

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.6 (R-3.4) (5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), dplyr
Imports	data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
LinkingTo
Suggests	knitr, rmarkdown, testthat, multiHiCcompare
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/HiCcompare
BugReports	https://github.com/dozmorovlab/HiCcompare/issues
Depends On Me
Imports Me	multiHiCcompare, SpectralTAD, TADCompare
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiCcompare_1.18.0.tar.gz
Windows Binary	HiCcompare_1.18.0.zip (64-bit only)
macOS Binary (x86_64)	HiCcompare_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiCcompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiCcompare
Package Short Url	https://bioconductor.org/packages/HiCcompare/
Package Downloads Report	Download Stats