- Home
- Bioconductor 3.9
- Software Packages
- HiCBricks
HiCBricks
This package is for version 3.9 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: 3.9
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], Ilario Tagliaferri [ctb]
Maintainer: Koustav Pal <koustav.pal at ifom.eu>
citation("HiCBricks")):
Installation
To install this package, start R (version "3.6") 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")
Details
See More
Package Archives
Follow Installation instructions to use this package in your R session.