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Dependencies
- anndata >=0.10.8
- certifi
- fast-array-utils >=1.4
- h5py >=3.11
- joblib
- legacy-api-wrap >=1.5
- matplotlib >=3.9
- natsort
- networkx >=2.8.8
- numba >=0.60
- numpy >=2
- packaging >=25
- pandas >=2.3
- patsy
- pynndescent >=0.5.13
- scikit-learn >=1.6
- scipy >=1.13
- seaborn >=0.13.2
- session-info2
- statsmodels >=0.14.5
- tqdm
- typing-extensions
- umap-learn >=0.5.12
21 optional dependencies
- anndata[dask-ml]
- anndata[dask]
- bbknn[bbknn]
- colour-science[plotting]
- cudf[rapids]
- cugraph[rapids]
- cuml[rapids]
- dask[dask-ml]
- dask[dask]
- dask-ml[dask-ml]
- harmonypy[harmony]
- igraph[louvain]
- igraph[leiden]
- igraph[paga]
- leidenalg[leiden]
- louvain[louvain]
- magic-impute[magic]
- scanorama[scanorama]
- scikit-image[scrublet]
- scikit-misc[skmisc]
- setuptools[louvain]
Used By
- scvi-tools
- tiledbsoma
- spatialdata-plot
- squidpy
- sure-tools
- spatialdata-io
- muon
- napari-spatialdata
- liana
- scvelo
- celltypist
- scib-metrics
- scib
- omicverse
- clustassesspy
- single-cell-metabolomics
- cellrank
- scimap
- lingergrn
- cell-eval
- sciv
- scellrun
- aiagents4pharma
- pertpy
- densityflow2
- scirpy
- tcrsift
- palantir
- densityflowmo
- exprmat
- rapids-singlecell
- linkapy
- sopa
- spatools
- step-kit
- sccross
- scgpt
- deeplife-toolkit
- celescope
- pyxenium
- uce-model
- cellphonedb
- doubletdetection
- celloracle
- stat-agent
- densityflow
- infercnvpy
- cell-load
- celldega
- hide-deconv