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: Model zoo for genomics

Model zoo for genomics

Kipoi overview figure

Kipoi (pronounce: kípi; from the Greek κήποι: gardens) is an API and a repository of ready-to-use trained models for regulatory genomics. It currently contains 2062 different models, covering canonical predictive tasks in transcriptional and post-transcriptional gene regulation. Kipoi's API is implemented as a python package (github.com/kipoi/kipoi) and it is also accessible from the command line or R.


Numbers

# of models: 2062

# of model groups: 19

# of contributors: 7

# of model groups supporting postprocessing:

  • Variant effect prediction: 12/19

Model groups by framework

Model groups by tag


Getting Started

Use models

Learn more

Contribute models

  • Install git-lfs: $ conda install -c conda-forge git-lfs && git lfs install
  • Install Kipoi: $ pip install kipoi
  • Run $ kipoi ls
  • Explore the models locally at ~/.kipoi/models
  • Add the model to ~/.kipoi/models/ (copy&edit the existing model or run kipoi init)
  • Test the model: kipoi test ~/.kipoi/models/my_model
  • Submit the pull-request to github.com/kipoi/models
Learn more

Contribute code