scalex.data.preprocessing

scalex.data.preprocessing(adata, profile='RNA', min_features=600, min_cells=3, target_sum=None, n_top_features=None, backed=False, chunk_size=20000, log=None)

Preprocessing single-cell data

Parameters:

• adata (AnnData) – An AnnData matrice of shape n_obs x n_vars. Rows correspond to cells and columns to genes.

• profile (str) – Specify the single-cell profile type, RNA or ATAC, Default: RNA.

• min_features (int) – Filtered out cells that are detected in less than n genes. Default: 100.

• min_cells (int) – Filtered out genes that are detected in less than n cells. Default: 3.

• target_sum (Optional[int]) – After normalization, each cell has a total count equal to target_sum. If None, total count of each cell equal to the median of total counts for cells before normalization.

• n_top_features – Number of highly-variable genes to keep. Default: 2000.

• chunk_size (int) – Number of samples from the same batch to transform. Default: 20000.

• log – If log, record each operation in the log file. Default: None.

Return type:

The AnnData object after preprocessing.