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HiCaptuRe

This is the development version of HiCaptuRe; to use it, please install the devel version of Bioconductor.

HiCaptuRe: Manipulating and integrating Capture Hi-C data


Bioconductor version: Development (3.22)

Capture Hi-C is a set of techniques that enable the detection of genomic interactions involving regions of interest, known as baits. By focusing on selected loci, these approaches reduce sequencing costs while maintaining high resolution at the level of restriction fragments. HiCaptuRe provides tools to import, annotate, manipulate, and export Capture Hi-C data. The package accounts for the specific structure of bait–otherEnd interactions, facilitates integration with other omics datasets, and enables comparison across samples and conditions.

Author: Laureano Tomas-Daza [aut, cre] ORCID iD ORCID: 0000-0002-6127-1694

Maintainer: Laureano Tomas-Daza <lauretomas at gmail.com>

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

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("HiCaptuRe")

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("HiCaptuRe")
Functions HTML R Script
Introduction HTML R Script
Reference Manual PDF

Details

biocViews DataImport, Epigenetics, HiC, Sequencing, Software
Version 0.99.15
In Bioconductor since BioC 3.22 (R-4.5)
License GPL-3
Depends R (>= 4.5.0)
Imports Biostrings, BSgenome, cli, data.table, dplyr, GenomeInfoDb, GenomicInteractions, GenomicRanges, InteractionSet, ggplot2, ggpubr, ggVennDiagram, gplots, igraph, IRanges, memoise, methods, S4Vectors, stringr, tibble, tidyr, UpSetR, utils
System Requirements
URL https://github.com/LaureTomas/HiCaptuRe
Bug Reports https://github.com/LaureTomas/HiCaptuRe/issues
See More
Suggests BSgenome.Hsapiens.NCBI.GRCh38, knitr, rmarkdown, DT, testthat, BiocStyle, kableExtra
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package HiCaptuRe_0.99.15.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64) HiCaptuRe_0.99.15.tgz
macOS Binary (arm64) HiCaptuRe_0.99.15.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCaptuRe
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCaptuRe
Bioc Package Browser https://code.bioconductor.org/browse/HiCaptuRe/
Package Short Url https://bioconductor.org/packages/HiCaptuRe/
Package Downloads Report Download Stats