HiContacts
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HiContacts.
Analysing cool files in R with HiContacts
Bioconductor version: 3.19
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Author: Jacques Serizay [aut, cre]
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
Citation (from within R, enter
citation("HiContacts")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.6.0 |
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_1.6.0.tar.gz |
Windows Binary (x86_64) | HiContacts_1.6.0.zip (64-bit only) |
macOS Binary (x86_64) | HiContacts_1.6.0.tgz |
macOS Binary (arm64) | HiContacts_1.6.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HiContacts |
Source Repository (Developer Access) | git clone [email protected]:packages/HiContacts |
Bioc Package Browser | https://code.bioconductor.org/browse/HiContacts/ |
Package Short Url | https://bioconductor.org/packages/HiContacts/ |
Package Downloads Report | Download Stats |