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HiCBricks

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

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


Bioconductor version: Development (3.19)

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>

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

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

Details

biocViews DataImport, HiC, Infrastructure, Sequencing, Software, Technology
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown
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Imports Me bnbc
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Package Archives

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

Source Package HiCBricks_1.21.0.tar.gz
Windows Binary HiCBricks_1.21.0.zip
macOS Binary (x86_64) HiCBricks_1.21.0.tgz
macOS Binary (arm64)
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