requirements.txt

# To ensure app dependencies are ported from your virtual environment/host machine into your container, run 'pip freeze > requirements.txt' in the terminal to overwrite this file
loompy
numpy
pytz
tqdm>=4.27 # same as transfomers

# Transformers
datasets
tensorflow # needed for Tensorboard logging
tensorrt # Tensorflow integration with NVIDIA GPUs
torch
accelerate>=0.20.1 # same as transfomers
transformers==4.31.0
deepspeed

# insilico_perturber_stats.py
statsmodels
seaborn
scikit-learn
scipy

# emb_extractor.py
anndata
scanpy
seaborn

# tokenizer
ray==2.6.3