# DenseCall2 dependencies
torch==2.9.1
torchvision==0.24.1
torchaudio==2.9.1
numpy==1.23.5
pandas==1.5.3
scipy==1.14.1
Cython==0.29.21
setuptools==67.6.1
ont-bonito==1.0.0
ont-fast5-api==4.1.3
pysam==0.21.0
pyslow5==1.3.1
pyfaidx==0.9.0.4
fast-ctc-decode==0.3.5
mappy
parasail==1.3.4
pod5
toml==0.10.2
pyyaml
h5py
scikit-learn
tqdm>4,<5
requests~=2.32.2
python-dateutil==2.8.2
matplotlib==3.10.8
seaborn==0.13.2
torchmetrics==1.9.0
pytorch-ranger==0.1.1
muon_optimizer==0.1.0
accelerate
transformers
tensorboard
pyBigWig==0.3.25
polars
plotnine==0.12.4
patchworklib==0.6.3
tabulate==0.9.0
statsmodels
torch_pruning==1.3.7
ruptures==1.1.9
tslearn==0.6.3
dtaidistance==2.3.11
rotary-embedding-torch==0.8.3
memory-efficient-attention-pytorch==0.1.6
jax
pyranges==0.1.4
fitter==1.7.1
gtfparse==2.0.1
biopython==1.86
pyabf
deap==1.4.1
igv==0.9.6
nltk==3.9.1
hyperopt
debugpy==1.8.8
onnxruntime-gpu==1.22.0
onnx-simplifier==0.4.36
onnx2torch==1.5.14
onnxconverter-common==1.14.0
onnxmltools==1.12.0
onnxscript==0.5.1
