Simple web browser to visualize HiC tracks
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README.md

HiCBrowser : A simple web browser to visualize Hi-C and other genomic tracks

Fidel Ramirez, José Villaveces, Vivek Bhardwaj

Installation

You can install HiCBrowser using pip :

pip install git+https://github.com/deeptools/HiCBrowser

You can also download/clone this GitHub repository and run the setup.py script inside :

cd HiCBrowser
python setup.py install -f

If you have Docker installed on your computer you can also use our Docker HiCBrowser Image. You can start a production ready HiCBrowser instance with:

docker run --rm -i -t -p 80:80 bgruening/docker-hicbrowser

For more information about the Docker image please refer to https://github.com/maxplanck-ie/docker-hicbrowser#usage

Usage

Install HiCExplorer

HiCBrowser works using HiCExplorer in the background. Thus, you need to install HiCExplorer first.

If HiCExplorer and or HiCBrowser is not properly installed (by running setup.py) it may be required to set the $PYTHONPATH. Specially for development it is quite convenient not to install the packages:

# ON COMMAND LINE
export PYTHONPATH=/path/to/HiCExplorer:/path/to/HiCBrowser

Test run

The folder example_browser contains all data and config files to run the browser. This is Drosophila melanogaster data only for chromosome X. To start the example server simply type:

cd example_browser
bash run_server.sh

Prepare files

HiCBrowser needs three config files.

  • region tracks : To visualize all genomic tracks for given regions. (eg. gene_tracks.ini)
  • gene tracks : To visualize TADs near given gene. (eg. region_tracks.ini)
  • browser config file : To providing information about directories to save images and the two tracks above. (eg. browserConfig.ini)

We have provided example for each of these files with the package, as shown above. For a full documentation of what types of data can be plotted in the region tracks and for extended examples please look at the documentation of the plotTADs function of HiCExplorer

Run

To run the browser, simply run runBrowser command, as shown below.

# --config = browser config file
# --port = localhost port to run the server

runBrowser --config browserConfig.ini --port 8888 --numProcessors 10 

Help

Contact our google Group deeptools@googlegroups.com for further help with HiCBrowser or HiCExplorer.