HiContacts

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

Analysing cool files in R with HiContacts

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DOI: 10.18129/B9.bioc.HiContacts

Bioconductor version: Development (3.23)

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

Author: Jacques Serizay [aut, cre] ORCID iD ORCID: 0000-0002-4295-0624

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

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

Installation

To install this package, start R (version "4.6") 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")

Introduction to HiContacts HTML R Script

Reference Manual PDF

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNA3DStructure, HiC, Software

Version 1.13.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License MIT + file LICENSE

Depends R (>= 4.2), HiCExperiment

Imports InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils

System Requirements

URL https://github.com/js2264/HiContacts

Bug Reports https://github.com/js2264/HiContacts/issues

Suggests HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me HiCExperiment

Links To Me

Build Report Build Report

Package Archives

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

Source Package HiContacts_1.13.0.tar.gz

Windows Binary (x86_64)

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

Bioc Package Browser https://code.bioconductor.org/browse/HiContacts/

Package Short Url https://bioconductor.org/packages/HiContacts/

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