multiHiCcompare

DOI: 10.18129/B9.bioc.multiHiCcompare    

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

Bioconductor version: Release (3.12)

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>

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

Installation

To install this package, start R (version "4.0") 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 1.8.0
In Bioconductor since BioC 3.8 (R-3.5) (2 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
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 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_1.8.0.tar.gz
Windows Binary multiHiCcompare_1.8.0.zip
macOS 10.13 (High Sierra) multiHiCcompare_1.8.0.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

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