Bering.tools.cell_analyze

Bering.tools.cell_analyze(adata, min_counts=10, target_sum=1000, n_neighbors=10)[source]

Run a standard analysis pipeline from single-cell data with raw counts. The pipeline includes: - Filter cells with low counts; - Normalize total counts; - Scale counts; - PCA; - Neighbor graph construction; - UMAP; - Leiden clustering.

Parameters:

  • adata (AnnData) – Anndata object. It can be the output of cell_annotation() function.

  • min_counts (int) – Minimum number of counts for a gene to be considered

  • target_sum (int) – Target sum of counts for normalization

  • n_neighbors (int) – Number of neighbors for KNN graph construction

Returns:

: adata: AnnData

Anndata object with updated fields