multiHiCcompare

DOI: 10.18129/B9.bioc.multiHiCcompare    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see multiHiCcompare.

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

Bioconductor version: 3.15

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.

Author: John Stansfield <stansfieldjc 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("multiHiCcompare")

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("multiHiCcompare")

 

HTML	R Script	juiceboxVisualization
HTML	R Script	multiHiCcompare
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.8 (R-3.5) (4 years)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/dozmorovlab/multiHiCcompare
BugReports	https://github.com/dozmorovlab/multiHiCcompare/issues
Depends On Me
Imports Me
Suggests Me	HiCcompare
Links To Me
Build Report

Package Archives

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

Source Package	multiHiCcompare_1.14.0.tar.gz
Windows Binary	multiHiCcompare_1.14.0.zip
macOS Binary (x86_64)	multiHiCcompare_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multiHiCcompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multiHiCcompare
Package Short Url	https://bioconductor.org/packages/multiHiCcompare/
Package Downloads Report	Download Stats