hicrep

This package is for version 3.9 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: 3.9

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 pairwise 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]

Maintainer: Tao Yang <xadmyangt at gmail.com>

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

Installation

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


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

BiocManager::install("hicrep")

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("hicrep")
Evaluate reproducibility of Hi-C data with `hicrep` HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews HiC, QualityControl, Sequencing, Software
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>= 2.0)
Depends R (>= 3.4)
Imports stats
System Requirements
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Suggests knitr, rmarkdown, testthat
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Depends On Me
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Package Archives

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

Source Package hicrep_1.8.0.tar.gz
Windows Binary hicrep_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) hicrep_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hicrep
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hicrep
Bioc Package Browser https://code.bioconductor.org/browse/hicrep/
Package Short Url https://bioconductor.org/packages/hicrep/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive