HiCBricks

DOI: 10.18129/B9.bioc.HiCBricks    

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

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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 1.4.0
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
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_1.4.0.tar.gz
Windows Binary HiCBricks_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) HiCBricks_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiCBricks
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiCBricks
Package Short Url https://bioconductor.org/packages/HiCBricks/
Package Downloads Report Download Stats

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