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("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 | ||
| LICENSE | Text |
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 |
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_1.4.0.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 [email protected]:packages/HiCool |
| Bioc Package Browser | https://code.bioconductor.org/browse/HiCool/ |
| Package Short Url | https://bioconductor.org/packages/HiCool/ |
| Package Downloads Report | Download Stats |