multiHiCcompare

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

Bioconductor version: Release (3.19)

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

Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>

Citation (from within R, enter citation("multiHiCcompare")):

Installation

To install this package, start R (version "4.4") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.22.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 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
System Requirements
URL	https://github.com/dozmorovlab/multiHiCcompare
Bug Reports	https://github.com/dozmorovlab/multiHiCcompare/issues

Suggests	knitr, rmarkdown, testthat, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me	HiCDOC, OHCA
Suggests Me	HiCcompare
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	multiHiCcompare_1.22.0.tar.gz
Windows Binary (x86_64)	multiHiCcompare_1.22.0.zip
macOS Binary (x86_64)	multiHiCcompare_1.22.0.tgz
macOS Binary (arm64)	multiHiCcompare_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/multiHiCcompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/multiHiCcompare
Bioc Package Browser	https://code.bioconductor.org/browse/multiHiCcompare/
Package Short Url	https://bioconductor.org/packages/multiHiCcompare/
Package Downloads Report	Download Stats