Model group Models Authors Contributed by Type Cite as License Tags
Model group Models Authors Contributed by Type Cite as License Tags
APARENT 2 Nicholas Bogard et al. Shabnam Sadegharmaki et al. None MIT
AttentiveChrome 55 Ritambhara Singh et al. Jack Lanchantin et al. pytorch MIT RNA expression
BPNet-OSKN 1 Ziga Avsec Ziga Avsec None MIT DNA binding
Basenji 1 David R. Kelley Ziga Avsec tensorflow Apache License v2 RNA expression, Histone modification, DNA accessibility
Basset 1 David R. Kelley 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 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 Roman Kreuzhuber keras
MIT DNA methylation
DeepFlyBrain 1 Ibrahim Ihsan Taskiran et al. Ibrahim Ihsan Taskiran et al. None TBA MIT
DeepMEL 3 Ibrahim Ihsan Taskiran et al. Ibrahim Ihsan Taskiran et al. None
DeepSEA 3 Jian Zhou et al. Roman Kreuzhuber None, pytorch
Non-comercial, CC-BY 3.0 Histone modification, DNA binding, DNA accessibility
DeepSTARR 1 Bernardo P. de Almeida Bernardo P. de Almeida None MIT
Divergent421 1 Nancy Xu Nancy Xu None MIT DNA accessibility
FactorNet 30 Daniel Quang et al. Ziga Avsec keras MIT DNA binding
Framepool 1 Alexander Karollus Alexander Karollus None MIT Translation
HAL 1 Alexander B. Rosenberg Jun Cheng et al. None MIT RNA splicing
KipoiSplice 2 Ziga Avsec et al. Ziga Avsec et al. sklearn MIT RNA splicing
MMSplice 5 Jun Cheng Jun Cheng custom MIT RNA splicing
MPRA-DragoNN 2 Rajiv Movva, Surag Nair Rajiv Movva, Surag Nair None MIT RNA expression
MaxEntScan 2 Gene Yeo et al. Jun Cheng et al. None MIT RNA splicing
Optimus_5Prime 1 Paul J. Sample Ban Wang None MIT Translation
SeqVec 3 Michael Heinzinger, Ahmed Elnaggar et al. Michael Heinzinger, Ahmed Elnaggar et al. None
MIT Protein properties, Protein structure
SiSp 1 Lara Urban Lara Urban keras MIT RNA splicing
TREDNet 4 Sanjarbek Hudaiberdiev Sanjarbek Hudaiberdiev None CC-BY-ND
Xpresso 5 Vikram Agarwal Vikram Agarwal None MIT
a2z-chromatin 2 Travis Wrightsman Travis Wrightsman None MIT DNA accessibility, DNA methylation, Plants
deepTarget 1 Byunghan Lee et al. Ziga Avsec None GPL-v3 RNA binding
epidermal_basset 60 Daniel Kim Daniel Kim None MIT
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 DNA binding
pwm_HOCOMOCO 600 Ivan V. Kulakovskiy Ziga Avsec keras MIT DNA binding
rbp_eclip 102 Ziga Avsec Ziga Avsec keras MIT RNA binding
scbasset 1 Han Yuan, David R. Kelley Han Yuan keras Apache License 2.0 scATAC accessibility

Kipoi models

CircleCI DOI

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

Contributing models

  1. Install kipoi:

    pip install kipoi

  2. Run kipoi ls. This will checkout the kipoi/models repo to ~/.kipoi/models)

  3. Follow the instructions on contributing/Getting started.

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/
        auto_update: True

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