DOI: 10.18129/B9.bioc.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 (3.13)

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")):


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biocViews DataImport, HiC, Infrastructure, Sequencing, Software, Technology
Version 1.9.0
In Bioconductor since BioC 3.8 (R-3.5) (2 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
Suggests BiocStyle, knitr, rmarkdown
Depends On Me
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Source Package HiCBricks_1.9.0.tar.gz
Windows Binary HiCBricks_1.9.0.zip
macOS 10.13 (High Sierra) HiCBricks_1.9.0.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/
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