HiCaptuRe
This is the development version of HiCaptuRe; for the stable release version, see HiCaptuRe.
HiCaptuRe: Manipulating and integrating Capture Hi-C data
Bioconductor version: Development (3.24)
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]
Maintainer: Laureano Tomas-Daza <lauretomas at gmail.com>
citation("HiCaptuRe")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Epigenetics, HiC, Sequencing, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | HiCaptuRe_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | HiCaptuRe_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | HiCaptuRe_1.3.0.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 |