HiCBricks

DOI: 10.18129/B9.bioc.HiCBricks    

This package is for version 3.8 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: 3.8

A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.

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

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

Installation

To install this package, start R (version "3.5") 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")

 

PDF	R Script	HiCBricks
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, HiC, Infrastructure, Sequencing, Software, Technology
Version	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5), utils, curl, rhdf5, R6, grid
Imports	ggplot2, viridis, RColorBrewer, scales, reshape2, stringr, data.table, GenomeInfoDb, GenomicRanges, stats, IRanges, grDevices, S4Vectors, digest, BiocFileCache, rappdirs
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Package Archives

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

Source Package	HiCBricks_1.0.0.tar.gz
Windows Binary	HiCBricks_1.0.0.zip
Mac OS X 10.11 (El Capitan)	HiCBricks_1.0.0.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	http://bioconductor.org/packages/HiCBricks/
Package Downloads Report	Download Stats