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 (3.21)
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Author: Jacques Serizay [aut, cre] (ORCID:
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
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")| Introduction to HiContacts | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DNA3DStructure, HiC, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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.
| Source Package | HiContacts_1.9.0.tar.gz |
| Windows Binary (x86_64) | HiContacts_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | HiContacts_1.9.0.tgz |
| macOS Binary (arm64) | HiContacts_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiContacts |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiContacts |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiContacts/ |
| Package Short Url | https://bioconductor.org/packages/HiContacts/ |
| Package Downloads Report | Download Stats |