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Co-visualisation of Hi-C with signal track data

Visualize Hi-C with any bigwig or bedGraph to combine both forms of data in a single image.

Bigwig

• Values > 0 (ChIP-seq, RNA-seq, etc.)
• chr | start | stop | value

bedGraph

• Values below and above 0 (Hi-C Compartment calls)
• chr | start | stop | value

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Web version

A light version of HiCrayon that allows import of publically availble Hi-C maps, bigwigs through URL eg. from ENCODE (https://www.encodeproject.org/), and locally stored small bedGraph files.

https://jrowleylab.com/HiCrayon/

To fully avail of the utility of HiCrayon, please proceed with installation below

Quick-start

Singularity

Singularity allows deployment of HiCrayon using a container so you don't need to worry about software compatibility issues.

Build singularity image from docker image

Build a singularity container from a docker image.

1. singularity build hicrayon.sif docker://nolandocker/hicrayon

Clone the hicrayon git repository.

2. git clone https://github.com/JRowleyLab/HiCrayon.git

cd into the HiCrayon directory and run the app inside the container

3. singularity exec ~/Containers/hicrayon.sif R -e "shiny::runApp('app.R', launch.browser=F, port = 3838)"

Additional parameters:

• if you'd like to attach a directory outside of your own: -B /:/filesystem/
• host application to allow access on another device (beware security risks): shiny::runApp(..., host="IPADDRESS")

Conda (Not recommended)

1. Create a conda environment with the hicrayon yaml file

conda create -n hicrayon hicrayon.yml

2. conda activate hicrayon

Clone the hicrayon git repo and cd into the repo

3. git clone https://github.com/JRowleyLab/HiCrayon.git

Run HiCrayon

4. R -e 'shiny::runApp("app.R", launch.browser=F)'

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Examples

Accurately visualize protein binding in Hi-C Maps

Reveal distinct layers of multi-state 3D chromatin organization.

Accurately demonstrate chromatin changes in differentiation

Visualize chromatin loops