multiHiCcompare

DOI: 10.18129/B9.bioc.multiHiCcompare    

This package is for version 3.9 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: 3.9

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 [aut, cre], Mikhail Dozmorov [aut]

Maintainer: John Stansfield <stansfieldjc at vcu.edu>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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	multiHiCcompare Vignette
HTML	R Script	Visualizing results in Juicebox
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	MIT + file LICENSE
Depends	R (>= 3.5.0)
Imports	data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL
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_1.2.0.tar.gz
Windows Binary	multiHiCcompare_1.2.0.zip
Mac OS X 10.11 (El Capitan)	multiHiCcompare_1.2.0.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