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multiHiCcompare

This is the development version of multiHiCcompare; for the stable release version, see multiHiCcompare.

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


Bioconductor version: Development (3.20)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews HiC, Normalization, Sequencing, Software
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
See More
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_1.23.0.tar.gz
Windows Binary multiHiCcompare_1.23.0.zip
macOS Binary (x86_64) multiHiCcompare_1.23.0.tgz
macOS Binary (arm64) multiHiCcompare_1.23.0.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