RBP Encode eCLIP

This repository contains RBP eCLIP data from Encode in "interval" format (for space eficiency reasons), notebook and a python script:

• create_csv_datasets.ipynb for reproducing creation of "interval" dataset and
• add_fasta.py for adding fasta sequences to the dataset.

Usage

Repository contains only partial data to save space. To get the full dataset (with sequences) you need to run add_fasta.py script. Result is stored in rbp_encode_eclip.csv file.

# clone this repository
git clone https://github.com/ML-Bioinfo-CEITEC/rbp_encode_eclip.git
cd rbp_encode_eclip

# create virtual environment
virtualenv venv --python=python3.8
source venv/bin/activate

# install dependencies
pip install genomic_benchmarks

# create final dataset
python add_fasta.py