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Peax-Avocado

This is a custom encoder model to use Avocado in Peax

Get Started

  1. Follow the instructions at https://github.com/flekschas/peax/blob/develop/README.md#installation to install Peax.

  2. Outside of Peax, clone this repo.

git clone https://github.com/flekschas/peax-avocado
  1. Download an Avocado model. E.g.:
cd peax-avocado
python download-avocado.py chr1

Note: download-avocado.py requires that you activated the px environment from Peax!

  1. Symlink peax-avocado into Peax.
cd ../peax
ln -s ../peax-avocado avocado
  1. Download the data that you want to explore and configure Peax. As an example do:
cd avocado
python download-example-data.py

Note: download-example-data.py requires that you activated the px environment from Peax!

  1. Start Peax.
python start.py -b avocado -c avocado/configs/e116-dnase-h3k27ac.json

Note: the configuration file corresponds to the example data from step 5.

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Avocado encoder model for Peax

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