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Dependencies
- aiohttp >=3.8.0
- anndata >=0.11.0
- click >=8.0.0
- igraph >=0.9.0
- jinja2 >=3.0.0
- leidenalg >=0.8.0
- matplotlib >=3.5.0
- mcp >=1.17.0
- numpy >=1.21.0
- pandas >=1.3.0
- pillow >=8.0.0
- pydantic <3.0,>=2.0.0
- scanpy <2.0,>=1.9.0
- scikit-learn >=1.0.0
- scipy >=1.7.0
- seaborn >=0.11.0
- squidpy >=1.2.0
- umap-learn >=0.5.0
69 optional dependencies
- adjusttext[full]
- anndata2ri[full]
- bbknn[full]
- bbknn[integration]
- black[dev]
- cell2location[full]
- cell2location[deconvolution]
- celldex[full]
- cellphonedb[cell-communication]
- cellphonedb[full]
- cellrank[full]
- enrichmap[full]
- esda[full]
- esda[spatial-stats]
- fastccc[full]
- fastccc[cell-communication]
- flashdeconv[full]
- flashdeconv[deconvolution]
- graphst[full]
- gseapy[full]
- harmonypy[full]
- harmonypy[integration]
- infercnvpy[full]
- isort[dev]
- liana[full]
- liana[cell-communication]
- libpysal[spatial-stats]
- libpysal[full]
- mllmcelltype[full]
- mudata[full]
- mudata[deep-learning]
- mypy[dev]
- networkx[full]
- networkx[spatial-stats]
- palantir[full]
- paste-bio[full]
- petsc4py[hpc]
- pot[full]
- pre-commit[dev]
- pybanksy[spatial-domains]
- pydeseq2[full]
- pygam[full]
- pysal[full]
- pysal[spatial-stats]
- pytest[dev]
- pytest-asyncio[dev]
- rpy2[full]
- ruff[dev]
- scanorama[full]
- scanorama[integration]
- scikit-gstat[full]
- scikit-misc[full]
- scvelo[full]
- scvelo[velocity]
- scvi-tools[deep-learning]
- scvi-tools[full]
- singlecellexperiment[full]
- singler[full]
- slepc4py[hpc]
- spagcn[spatial-domains]
- spatialdata[full]
- spatialde[full]
- splot[full]
- statannotations[full]
- statsmodels[full]
- statsmodels[spatial-stats]
- tangram-sc[full]
- torch[full]
- torch[deep-learning]