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HiCool

This is the development version of HiCool; for the stable release version, see HiCool.

HiCool


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("HiCool")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
HiCool HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews DNA3DStructure, DataImport, HiC, Software
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
System Requirements
URL https://github.com/js2264/HiCool
Bug Reports https://github.com/js2264/HiCool/issues
See More
Suggests HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me OHCA
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package HiCool_1.3.0.tar.gz
Windows Binary
macOS Binary (x86_64) HiCool_1.3.0.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