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 https://doi.org/10.1101/gr.227819.117 Apache License v2 RNA expression, Histone modification, DNA accessibility
Basset 1 David R. Kelley et al. Roman Kreuzhuber pytorch https://doi.org/10.1101/gr.200535.115 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 https://doi.org/10.1093/nar/gkx177 Apache License v2 DNA methylation
DeepBind 927 Babak Alipanahi et al. Johnny Israeli keras https://doi.org/10.1038/nbt.3300 BSD 3-Clause DNA binding
DeepCpG_DNA 5 Christof Angermueller et al. Roman Kreuzhuber keras https://doi.org/10.1186/s13059-017-1189-z
https://doi.org/10.5281/zenodo.1094823
MIT DNA methylation
DeepSEA 2 Jian Zhou et al. Roman Kreuzhuber pytorch https://doi.org/10.1038/nmeth.3547 CC-BY 3.0 Histone modification, DNA binding, DNA accessibility
Divergent421 1 Nancy Xu Nancy Xu None MIT DNA accessibility
FactorNet 30 Daniel Quang et al. Ziga Avsec keras https://doi.org/10.1101/151274 MIT DNA binding
HAL 1 Alexander B. Rosenberg et al. Jun Cheng et al. None https://doi.org/10.1016/j.cell.2015.09.054 MIT RNA splicing
KipoiSplice 2 Ziga Avsec et al. Ziga Avsec et al. sklearn https://doi.org/10.1101/375345 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 https://doi.org/10.1089/1066527041410418 MIT RNA splicing
Optimus_5Prime 1 Paul J. Sample et al. Ban Wang None https://doi.org/10.1101/310375 MIT Translation
SiSp 1 Stephanie Maria Linker et al. Lara Urban keras https://doi.org/10.1101/328138 MIT RNA splicing
deepTarget 1 Byunghan Lee et al. Ziga Avsec None https://arxiv.org/pdf/1603.09123.pdf GPL-v3 RNA binding
extended_coda 1 Pang Wei Koh et al. Johnny Israeli keras https://doi.org/10.1093/bioinformatics/btx243 MIT Histone modification
labranchor 1 Joseph M. Paggi et al. Jun Cheng keras https://doi.org/10.1101/185868 CC BY-NC 4.0 RNA splicing
lsgkm-SVM 322 Dongwon Lee Roman Kreuzhuber None https://doi.org/10.1093/bioinformatics/btw142 MIT
pwm_HOCOMOCO 600 Ivan V. Kulakovskiy et al. Ziga Avsec keras https://doi.org/10.1093/nar/gkv1249 MIT DNA binding
rbp_eclip 112 Žiga Avsec et al. Žiga Avsec keras https://doi.org/10.1093/bioinformatics/btx727 MIT RNA binding

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 http://kipoi.org/models. See kipoi/README.md 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 (https://github.com/kipoi/models) is included in the Kipoi config file (~/.kipoi/config.yaml) by default:

# ~/.kipoi/config.yaml
model_sources:
    kipoi:
        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.