koustav-pal/HiCBlocks: Framework for Storing and Accessing Hi-C Data Through HDF Files

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.

Getting started

Package details

Bioconductor views DataImport HiC Infrastructure Sequencing Software Technology
MaintainerKoustav Pal <[email protected]>
LicenseMIT + file LICENSE
Version1.1.14
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("koustav-pal/HiCBlocks")
koustav-pal/HiCBlocks documentation built on March 19, 2019, 12:01 p.m.