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>

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

Installation

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

HiCBricks	PDF	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, HiC, Infrastructure, Sequencing, Software, Technology
Version	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (5.5 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
System Requirements
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Build Report	Build Report

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
Bioc Package Browser	https://code.bioconductor.org/browse/HiCBricks/
Package Short Url	https://bioconductor.org/packages/HiCBricks/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.8	Source Archive