Welcome to HiCrayon!
HiCrayon is a tool used to visualize the complex layering of chromatin organization across Hi-C, Micro-C, ChIP-seq, and CUT&RUN in a single image!
Use HiCrayon to create beautiful images and visualize 1D tracks on 2D matrices.
Build a singularity container from a docker image.
singularity build hicrayon.sif docker://nolandocker/hicrayon:v2
Clone the hicrayon git repository.
git clone https://github.com/JRowleyLab/HiCrayon.git
cd into the HiCrayon directory and run the app inside the container
singularity exec hicrayon_container.sif Rscript run.R
Under the sidebar option, Hi-C, at the bottom you'll see a button called 'Example Setup'. Click this and the application will automatically populate with the following data:
- Hi-C from a human colon cancer cell line.
- Three histone marks uploaded in bigwigs; H3K9me3, H3K27me3 and H3K27ac
- Eigenvector uploaded as a bedgraph.
All you need to do now is click 'Generate' at the bottom of the sidebar, and it will load in all the above data, do some HiCrayon stuff, and output the Hi-C map, but now it's colored by histone occupancy, and the eigenvector status!
Upload a Hi-C file from a local directory, or by importing through a URL and start visualizing! Detailed instructions on usage can be found here: Usage
A lite version of HiCrayon is available at:
jrowleylab.com/HiCrayon/This version supports ONLY small file uploads. Small Hi-C maps or 1D tracks can be uploaded, but we have implemented a size cap. However, published Hi-C maps and bigwigs from ENCODE (https://www.encodeproject.org/) are able to be visualized in their entirety.
To fully avail yourself of the utility of HiCrayon, please Install a local version of the app.
To install HiCrayon, we use containerized Singularity that allows for a portable, reproducible environment.
- [Singularity] is our primary method and has excellent documentation.
- [Conda] is also available but NOT recommended.
At least 10 gigabytes of storage are recommended for the installation of the application, singularity image, and storage of the large experiment files.
HiCrayon is available for public use and accompanies the publication https://doi.org/10.1101/2024.02.11.579821.
Please address questions to the primary author: bnolan@unmc.edu