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Dependencies
- anndata
- biopython
- broad-babel >=0.1
- cirpy
- huggingface-hub <1.0.0,>=0.35
- ipywidgets
- matplotlib
- numpy <3,>=1.26
- pandas >=2.2
- protobuf >=3.20
- pyarrow >=14.0.2
- pyensembl >=2.3.13
- pysam >=0.22
- rdkit
- requests
- scikit-learn >=1.3
- scipy >=1.11
- seaborn
- sentencepiece >=0.1.99
- session-info
- torch-geometric >=2.5
- transformers <5.0.0,>=4.45.0
87 optional dependencies
- arc-stack[stack]
- arc-state[state]
- boltz[boltz]
- borzoi-pytorch[all-cpu]
- borzoi-pytorch[all-cu121]
- borzoi-pytorch[all-cu124]
- borzoi-pytorch[all-cu128]
- borzoi-pytorch[seqmodels]
- borzoi-pytorch[all]
- cell-eval[eval]
- coverage[test]
- docutils[doc]
- enformer-pytorch[all-cu121]
- enformer-pytorch[all-cpu]
- enformer-pytorch[all]
- enformer-pytorch[seqmodels]
- enformer-pytorch[all-cu128]
- enformer-pytorch[all-cu124]
- esm[esm3]
- evo-model[evo]
- evo2[evo2]
- h5py[ppi]
- h5py[all-cu128]
- h5py[all-cu124]
- h5py[all-cu121]
- h5py[all-cpu]
- h5py[all]
- helical[helical]
- ipykernel[doc]
- ipython[doc]
- jump-portrait[morphology]
- jump-portrait[all]
- jump-portrait[all-cpu]
- jump-portrait[all-cu121]
- jump-portrait[all-cu124]
- jump-portrait[all-cu128]
- lamindb[lamindb]
- lamindb[all-cu128]
- lamindb[all-cu124]
- lamindb[all-cu121]
- lamindb[all]
- lamindb[all-cpu]
- mamba-ssm[caduceus]
- minimol[minimol]
- myst-nb[doc]
- pertpy[all-cu124]
- pertpy[all-cu121]
- pertpy[all-cpu]
- pertpy[all]
- pertpy[pertpy]
- pertpy[all-cu128]
- pillow[all-cu128]
- pillow[all-cu121]
- pillow[all-cu124]
- pillow[morphology]
- pillow[all]
- pillow[all-cpu]
- pre-commit[dev]
- pytest[test]
- pytest-mock[test]
- scanpy[all-cu121]
- scanpy[all]
- scanpy[all-cpu]
- scanpy[all-cu124]
- scanpy[all-cu128]
- scanpy[scanpy]
- setuptools[doc]
- sphinx[doc]
- sphinx-autodoc-typehints[doc]
- sphinx-book-theme[doc]
- sphinx-copybutton[doc]
- sphinx-tabs[doc]
- sphinxcontrib-bibtex[doc]
- sphinxext-opengraph[doc]
- torch[torch-cu124]
- torch[torch-cu128]
- torch[torch-cu130]
- torch[all-cu128]
- torch[all]
- torch[all-cpu]
- torch[all-cu121]
- torch[all-cu124]
- torch[torch]
- torch[torch-cpu]
- torch[torch-cu121]
- transformers[ntv3]
- twine[dev]