kipoi/examples

This repository contains different use-cases higlighting Kipoi. Accompanying presentation can be found here. Check out the readme in each sub-folder for more information. Please follow the steps bellow to setup your environment:

Setup

• Install miniconda or anaconda.
• Make sure you have the following packages installed:
  • conda:
    • conda install -y -c conda-forge jupyterlab
    • conda install -y nb_conda datrie
  • pip:
    • pip install numpy pandas matplotlib seaborn snakemake kipoi>=0.6.0
• Clone this repository: git clone https://github.com/kipoi/examples.git && cd examples

Verify Kipoi

Run:

• kipoi ls

This will list all the models and checkout the model source to ~/.kipoi/models.

Install the common environment

• kipoi env create shared/envs/kipoi-py3-keras2

Test the locally installed models

Activate the environment

source activate kipoi-shared__envs__kipoi-py3-keras2

Test all the used models in the tutorials:

kipoi test Basset --source=kipoi

kipoi test DeepSEA/predict --source=kipoi

kipoi test DeepBind/Homo_sapiens/TF/D00328.018_ChIP-seq_CTCF/ --source=kipoi

Next step: 1-predict

Links

• https://kipoi.org - website with pointers to the docs, white-paper and models.
• Workshop: MIA Workshop Broad institute 2018 - Accompanying slides for this tutorial.
• Gitter chat