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Baskerville

Sequential regulatory activity predictions with deep convolutional neural networks.

Baskerville provides researchers with tools to:

  1. Train deep convolutional neural networks to predict regulatory activity along very long chromosome-scale DNA sequences
  2. Score variants according to their predicted influence on regulatory activity across the sequence and/or for specific genes.
  3. Annotate the specific nucleotides that drive regulatory element function.

Documentations

Documentation page: https://calico.github.io/baskerville/index.html

Installation

git clone [email protected]:calico/baskerville.git cd baskerville pip install .

To set up the required environment variables: cd baskerville conda activate <conda_env> ./env_vars.sh

Note: Change the two lines of code at the top of './env_vars.sh' to the correct local paths.

Alternatively, the environment variables can be set manually:

export BASKERVILLE_DIR=/home/<user_path>/baskerville
export PATH=$BASKERVILLE_DIR/src/baskerville/scripts:$PATH
export PYTHONPATH=$BASKERVILLE_DIR/src/baskerville/scripts:$PYTHONPATH

export BASKERVILLE_CONDA=/home/<user>/anaconda3/etc/profile.d/conda.sh

Contacts

Dave Kelley (codeowner)