HiCBricks

HiCBricks is a R/Bioconductor package for handling high-resolution Hi-C datasets through HDF (Hierarchical Data Format) files. Read more about HDF here

HiCBricks greatly simplifies user handling of Hi-C contact matrices.
Forces users to adhere to a set of Hi-C analysis good-practices.
HiCBricks simplifies how users interaction with HDF files containing Hi-C contact matrices.

Features

Import Hi-C data in multiple data formats. Currently, NxN dimensional matrices, mcool files and sparse matrices are supported, with more to come.
Fetch different subset of the Hi-C data by their features with easy to use functions. Feature examples: by distance, matrix squares, rows or columns.
Keep user-defined annotations associated to the HDF files.
Use HiCBricks accessors to build more complex analysis such as TAD calling and visualizations.

Installation

To install the most stable development version from Bioconductor, run this from a R console. Note: R version >= 3.5 is required. This command will first installs BiocManager from CRAN. BiocManager is a convenient utility to install Bioconductor packages. Then, we install HiCBricks through BiocManager.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("HiCBricks", version = "3.11")

To install the stable release version from Bioconductor, run this from a R console.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("HiCBricks", version = "3.11")

To install the most cutting-edge stable version of HiCBricks, do this from a R console to download it directly from GitHub.

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_git("https://github.com/koustav-pal/HiCBricks")

Getting Started

To start working with HiCBricks, please checkout the vignette (tutorial) here, at the main Bioconductor website. It contains an in-depth walkthrough of almost all functions in HiCBricks and will guide users through the process of

Loading data from text 2D files.
Loading data from mcool files.
Loading data from sparse matrices.
Making TAD calls and spohisticated heatmaps with example functions built using HiCBricks accessor functions.

Development Notes

HiCBricks API is now stable. While we may move to sparse or feather representations later, this API will not change.
With Bioconductor release 3.10, a formal S4 class has been implemented for a better user experience.
With Bioconductor release 3.11, sparse matrix support has been implemented.

Future Roadmap

There are many new developments which are planned for future releases of HiCBricks. Broadly speaking,

I will try to implement read and export functions for as many new Hi-C data formats as possible. On top priority is HiCExplorer and .hic.

Contributing

If you would like to help out, let me know via email at koustav.pal@ifom.eu.