HiCool

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HiCool.

HiCool

Bioconductor version: 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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNA3DStructure, DataImport, HiC, Software

Version 1.4.0

In Bioconductor since BioC 3.17 (R-4.3) (1.5 years)

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 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_1.4.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) HiCool_1.4.0.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