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("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 | ||
| 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 | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |