HiCool

DOI: 10.18129/B9.bioc.HiCool  

HiCool

Bioconductor version: Release (3.17)

HiCool provides an R interface to process and normalize Hi-C paired-end fastq reads into .(m)cool files. .(m)cool is a compact, indexed HDF5 file format specifically tailored for efficiently storing HiC-based data. On top of processing fastq reads, HiCool provides a convenient reporting function to generate shareable reports summarizing Hi-C experiments and including quality controls.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HiCool")

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("HiCool")

 

HTML	R Script	HiCool
PDF		Reference Manual
Text		LICENSE

Details

biocViews	DNA3DStructure, DataImport, HiC, Software
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.2), HiCExperiment
Imports	BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet, vroom, basilisk, reticulate, rmarkdown, rmdformats, plotly, dplyr, stringr, sessioninfo, utils
LinkingTo
Suggests	HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/js2264/HiCool
BugReports	https://github.com/js2264/HiCool/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	HiCool_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)	HiCool_1.0.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/HiCool
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiCool
Bioc Package Browser	https://code.bioconductor.org/browse/HiCool/
Package Short Url	https://bioconductor.org/packages/HiCool/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive