hicrep

DOI: 10.18129/B9.bioc.hicrep    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see hicrep.

Measuring the reproducibility of Hi-C data

Bioconductor version: 3.12

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwiseß differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth. Compared to existing approaches, it consistently shows higher accuracy in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages than existing approaches. This R package `hicrep` implements our approach.

Author: Tao Yang [aut, cre], Fan Song [ctb]

Maintainer: Tao Yang <xadmyangt at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("hicrep")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	HiC, QualityControl, Sequencing, Software
Version	1.14.0
In Bioconductor since	BioC 3.5 (R-3.4) (4 years)
License	GPL (>= 2.0)
Depends	R (>= 3.3)
Imports	stats, rhdf5, Rcpp, rmarkdown, testthat, strawr
LinkingTo	Rcpp
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/hicrep
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hicrep
Package Short Url	https://bioconductor.org/packages/hicrep/
Package Downloads Report	Download Stats