HiContacts

DOI: 10.18129/B9.bioc.HiContacts  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HiContacts.

HiContacts: R interface to cool files

Bioconductor version: 3.16

HiContacts: R interface to (m)cool files and other Hi-C processed file formats. HiContacts provides a collection of tools to analyse and visualize Hi-C datasets. It can import data from pairs or (m)cool files.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("HiContacts")

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("HiContacts")

 

HTML	R Script	Introduction to HiContacts
PDF		Reference Manual
Text		LICENSE

Details

biocViews	DNA3DStructure, DataImport, HiC, Software
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	HiContactsData, InteractionSet, GenomicInteractions, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, BiocGenerics, methods, rhdf5, Matrix, vroom, tibble, tidyr, dplyr, glue, stringr, reticulate, ggplot2, ggrastr, scales
LinkingTo
Suggests	cowplot, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/js2264/HiContacts
BugReports	https://github.com/js2264/HiContacts/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiContacts_1.0.0.tar.gz
Windows Binary	HiContacts_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	HiContacts_1.0.0.tgz
macOS Binary (arm64)	HiContacts_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiContacts
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiContacts
Bioc Package Browser	https://code.bioconductor.org/browse/HiContacts/
Package Short Url	https://bioconductor.org/packages/HiContacts/
Package Downloads Report	Download Stats