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Bioconductor - HiContacts (development version)

HiContacts

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

Analysing cool files in R with HiContacts

Bioconductor version: Development (3.22)

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

Author: Jacques Serizay [aut, cre] 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 "4.5") 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")
Details biocViews DNA3DStructure, HiC, Software Version 1.11.0 In Bioconductor since BioC 3.16 (R-4.2) (2.5 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 See More 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 OHCA Suggests Me HiCExperiment, HiCool Links To Me Build Report Build Report Package Archives

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

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