HiCcompare

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

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Bioconductor version: Development (3.18)

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.

Author: Mikhail Dozmorov [aut, cre] , Kellen Cresswell [aut], John Stansfield [aut]

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

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

BiocManager::install("HiCcompare")

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("HiCcompare")

HiCcompare Usage Vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	HiC, Normalization, Sequencing, Software
Version	1.23.1
In Bioconductor since	BioC 3.6 (R-3.4) (6 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), dplyr
Imports	data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
Linking To
Suggests	knitr, rmarkdown, testthat, multiHiCcompare
System Requirements
Enhances
URL	https://github.com/dozmorovlab/HiCcompare
Bug Reports	https://github.com/dozmorovlab/HiCcompare/issues

Depends On Me
Imports Me	multiHiCcompare, SpectralTAD, TADCompare
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiCcompare_1.23.1.tar.gz
Windows Binary	HiCcompare_1.23.1.zip
macOS Binary (x86_64)	HiCcompare_1.23.1.tgz
macOS Binary (arm64)	HiCcompare_1.23.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiCcompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiCcompare
Bioc Package Browser	https://code.bioconductor.org/browse/HiCcompare/
Package Short Url	https://bioconductor.org/packages/HiCcompare/
Package Downloads Report	Download Stats