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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

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

Suggests	HiContacts, HiContactsData, AnnotationHub, BiocFileCache, BiocStyle, testthat, knitr, rmarkdown
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
Windows Binary
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/HiCool/
Package Downloads Report	Download Stats