HiCBricks

DOI: 10.18129/B9.bioc.HiCBricks  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HiCBricks.

Framework for Storing and Accessing Hi-C Data Through HDF Files

Bioconductor version: 3.16

HiCBricks is a library designed for handling large high-resolution Hi-C datasets. Over the years, the Hi-C field has experienced a rapid increase in the size and complexity of datasets. HiCBricks is meant to overcome the challenges related to the analysis of such large datasets within the R environment. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms. HiCBricks already incorporates example algorithms for calling domain boundaries and functions for high quality data visualization.

Author: Koustav Pal [aut, cre], Carmen Livi [ctb], Ilario Tagliaferri [ctb]

Maintainer: Koustav Pal <koustav.pal at ifom.eu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("HiCBricks")

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("HiCBricks")

 

HTML	R Script	IntroductionToHiCBricks.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, HiC, Infrastructure, Sequencing, Software, Technology
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6), utils, curl, rhdf5, R6, grid
Imports	ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils, readr, methods
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
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	HiCBricks_1.16.0.tar.gz
Windows Binary	HiCBricks_1.16.0.zip (64-bit only)
macOS Binary (x86_64)	HiCBricks_1.16.0.tgz
macOS Binary (arm64)	HiCBricks_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HiCBricks
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HiCBricks
Bioc Package Browser	https://code.bioconductor.org/browse/HiCBricks/
Package Short Url	https://bioconductor.org/packages/HiCBricks/
Package Downloads Report	Download Stats