Model group Models Authors Contributed by Type Cite as License Tags
Model group Models Authors Contributed by Type Cite as License Tags
Basenji 1 David R. Kelley et al. Ziga Avsec tensorflow Apache License v2 RNA expression, Histone modification, DNA accessibility
Basset 1 David R. Kelley et al. Roman Kreuzhuber pytorch MIT DNA accessibility
CleTimer 2 Leohnard Wachutka et al. Leohnard Wachutka et al. None Apache License v2 RNA splicing
CpGenie 51 Haoyang Zeng et al. Roman Kreuzhuber custom, keras Apache License v2 DNA methylation
DeepBind 927 Babak Alipanahi et al. Johnny Israeli keras BSD 3-Clause DNA binding
DeepCpG_DNA 5 Christof Angermueller et al. Roman Kreuzhuber keras
MIT DNA methylation
DeepSEA 2 Jian Zhou et al. Roman Kreuzhuber pytorch CC-BY 3.0 Histone modification, DNA binding, DNA accessibility
Divergent421 1 Nancy Xu Nancy Xu keras MIT DNA accessibility
FactorNet 30 Daniel Quang et al. Ziga Avsec keras MIT DNA binding
HAL 1 Alexander B. Rosenberg et al. Jun Cheng et al. None MIT RNA splicing
KipoiSplice 2 Ziga Avsec et al. Ziga Avsec et al. sklearn MIT RNA splicing
MMSplice 10 Jun Cheng et al. Jun Cheng et al. custom, keras MIT RNA splicing
MaxEntScan 2 Gene Yeo et al. Jun Cheng et al. None MIT RNA splicing
SiSp 1 Stephanie Maria Linker et al. Lara Urban keras MIT RNA splicing
deepTarget 1 Byunghan Lee et al. Ziga Avsec None GPL-v3 RNA binding
extended_coda 1 Pang Wei Koh et al. Johnny Israeli keras MIT Histone modification
labranchor 1 Joseph M. Paggi et al. Jun Cheng keras CC BY-NC 4.0 RNA splicing
lsgkm-SVM 322 Dongwon Lee Roman Kreuzhuber None MIT
pwm_HOCOMOCO 600 Ivan V. Kulakovskiy et al. Ziga Avsec keras MIT DNA binding
rbp_eclip 112 Žiga Avsec et al. Žiga Avsec keras MIT RNA binding

Kipoi models


This repository hosts predictive models for genomics and serves as a model source for Kipoi. Each folder containing the following files is considered to be a single model:

├──     # implements the dataloader
├── dataloader.yaml   # describes the dataloader
├── dataloader_files/      #/ files required by the dataloader
│   └── ...
├── model.yaml        # describes the model
├── model_files/           #/ files required by the model (like weights.h5 and arch.json)
│   └── ...
└── example_files/         #/ small example files used to test the model
    └── ...

Folders named *_files are tracked by Git Large File Storage (LFS). New models are added by simply submitting a pull-request to

Contributing models

1. Install Kipoi

  1. Install git-lfs
  2. Install kipoi
    • pip install kipoi
  3. Run kipoi ls (this will checkout the kipoi/models repo to ~/.kipoi/models)

2. Add the model

  1. cd ~/.kipoi/models
  2. Write the model: Create a new folder <my new model> containing all the required files
    • Option 1: Copy the existing model: cp -R <existing model> <my new model> & edit the copied files
    • Option 2: Run kipoi init, answer the questions & edit the created files
    • Option 3: mkdir <my new model> & write all the files from scratch
  3. Test the model
    • Step 1: kipoi test ~/.kipoi/models/my_new_model
    • Step 2: kipoi test-source kipoi --all -k my_new_model
  4. Commit your changes
    • cd ~/.kipoi/models && git commit -m "Added <my new model>"

3. Submit the pull-request

  1. Fork the repo on github (click on the Fork button)
  2. Add your fork as a git remote to ~/.kipoi/models
    • cd ~/.kipoi/models && git remote add fork<username>/models.git
  3. Push to your fork
    • git push fork master
  4. Submit a pull-request (click the New pull request button on your github fork -<username>/models>)

See docs/contributing getting started and docs/tutorials/contributing/models for more information.

Using models (to predict, score variants, build new models)

To explore available models, visit See kipoi/ and docs/using getting started for more information on how to programatically access the models from this repository using CLI, python or R.

Configuring local storage location

This model source ( is included in the Kipoi config file (~/.kipoi/config.yaml) by default:

# ~/.kipoi/config.yaml
        type: git-lfs
        remote_url: [email protected]:kipoi/models.git
        local_path: ~/.kipoi/models/

If you wish to keep the models stored elsewhere, edit the local_path accordingly.