OHCA

This is the released version of OHCA; for the devel version, see OHCA.

All versions

3.24 (devel), 3.23 (release)

Orchestrating Hi-C analysis with Bioconductor

Bioconductor version: Release (3.23)

The primary aim of this book is to introduce the R user to Hi-C analysis. This book starts with key concepts important for the analysis of chromatin conformation capture and then presents Bioconductor tools that can be leveraged to process, analyze, explore and visualize Hi-C data.

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

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

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

Jacques Serizay. OHCA: Orchestrating Hi-C analysis with Bioconductor. doi:10.18129/B9.bioc.OHCA, R package version 1.8.0, https://bioconductor.org/packages/OHCA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

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

BiocManager::install("OHCA")

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("OHCA")

Link to book	HTML
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNA3DStructure, FunctionalGenomics, HiC, Software
Version	1.8.0
In Bioconductor since	BioC 3.23 (R-4.6) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.4)
Imports	HiCExperiment, HiCool, HiContacts, HiContactsData, DNAZooData, fourDNData, plyinteractions, GenomicInteractions, terra, Rfast, WGCNA, diffHic, strawr, multiHiCcompare, TopDom, GOTHiC, BSgenome.Hsapiens.UCSC.hg38, ggbio, cowplot, patchwork, fs, knitr, BiocStyle, sessioninfo
System Requirements
URL	https://github.com/js2264/OHCA
Bug Reports	https://github.com/js2264/OHCA/issues

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Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/OHCA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OHCA
Package Short Url	https://bioconductor.org/packages/OHCA/
Package Downloads Report	Download Stats