HiCaptuRe
HiCaptuRe: Manipulating and integrating Capture Hi-C data
Bioconductor version: 3.24 · Package version: 1.3.8
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCaptuRe")Details
| Maintainer | Laureano Tomas-Daza <lauretomas@gmail.com> |
| Author | Laureano Tomas-Daza [aut, cre] (ORCID: <https://orcid.org/0000-0002-6127-1694>) |
| License | GPL-3 |
| URL | https://github.com/LaureTomas/HiCaptuRe |
| Bug Reports | https://github.com/LaureTomas/HiCaptuRe/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, Epigenetics, HiC, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/HiCaptuRe/ |
Citation
From within R, enter citation("HiCaptuRe"):
Laureano Tomas-Daza. HiCaptuRe: HiCaptuRe: Manipulating and integrating Capture Hi-C data. doi:10.18129/B9.bioc.HiCaptuRe, R package version 1.3.8, https://bioconductor.org/packages/HiCaptuRe.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiCaptuRe_1.3.8.tar.gz |
| Windows binary (x86_64) | HiCaptuRe_1.3.8.zip |
| macOS binary (arm64) | HiCaptuRe_1.3.8.tgz |
| macOS binary (x86_64) | HiCaptuRe_1.3.8.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: BiocGenerics, Biostrings, BSgenome, cli, data.table, dplyr, GenomeInfoDb, GenomicInteractions, GenomicRanges, InteractionSet, ggplot2, ggpubr, ggVennDiagram, gplots, igraph, IRanges, memoise, methods, S4Vectors, stringr, tibble, tidyr, UpSetR, utils
Suggests: BSgenome.Hsapiens.NCBI.GRCh38, knitr, rmarkdown, DT, testthat, BiocStyle, kableExtra