requirements.txt

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)