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requirements.txt
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requirements.txt
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typing_extensions
# main requirements for single-cell analysis
anndata>=0.7.5 # compatible with h5py v3.0 (v0.7.5)
scanpy>=1.5 # adapt to new anndata attributes (v1.5)
# for reading loom files with spliced/unspliced counts
loompy>=2.0.12 # introduced sparsity support (v2.0.12)
# for computing neighbor graph connectivities
umap-learn>=0.3.10 # removed numba warnings (v0.3.10)
# standard requirements for data analysis
numba>=0.41.0
numpy>=1.17 # extension/speedup in .nan_to_num, .exp (v1.17)
scipy>=1.4.1 # introduced PCA sparsity support (v1.4)
pandas>=0.23 # merging/sorting extensions (v0.23)
scikit-learn>=0.21.2 # bugfix in .utils.sparsefuncs (v0.21.2)
matplotlib>=3.3.0 # normalize in pie (v3.3.0)