A Demo for fine tuning the enformer-pytorch

NOTE: This repo is still under development.

Requirements

The Python>=3.8 is required. The required packages are listed in requirements.txt. You can install them by running the following command:

$ pip install -r requirements.txt

About the demo data

The demo data is in data folder. But due to the size limit of GitHub, it is not included in the repo. You can create your own Fasta and bigwig data, and change the path in relevant notebooks.

Generate the target regions for fine tuning

python scripts/generate_target_region.py data/Sus_scrofa.Sscrofa11.1.dna.toplevel.chr.fa data/target_regions.bed --block_size=98304 --limit_chroms="['chr1']"