HiContacts

DOI: 10.18129/B9.bioc.HiContacts    

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

HiContacts: R interface to cool files

Bioconductor version: Development (3.17)

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>

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

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("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 1.1.0
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_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HiContacts
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiContacts
Package Short Url https://bioconductor.org/packages/HiContacts/
Package Downloads Report Download Stats

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