scbulkde.engines.DEEngineBase

scbulkde.engines.DEEngineBase#

class scbulkde.engines.DEEngineBase#

Abstract base class for differential expression engines.

Subclass this to implement new DE backends.

Attributes table#

DEEngineBase.name: str = 'base'

Methods table#

run(counts, metadata, design_matrix, ...[, ...])

Run differential expression analysis.

Attributes#

DEEngineBase.name: str = 'base'#

Methods#

abstractmethod DEEngineBase.run(counts, metadata, design_matrix, design_formula, alpha, correction_method, *, gene_names=None, **kwargs)#

Run differential expression analysis.

Parameters:

  • counts (DataFrame | ndarray) – Gene expression counts (samples x genes). Can be DataFrame or numpy array. When numpy array is provided, gene_names must also be provided.

  • metadata (DataFrame) – Sample metadata with design variables.

  • design_matrix (DataFrame) – Design matrix for the regression model.

  • design_formula (str) – Design formula (e.g., “~condition” or “~condition+batch”).

  • alpha (float) – Significance threshold for adjusted p-values.

  • correction_method (str) – Method for multiple testing correction.

  • gene_names (ndarray | None (default: None)) – Gene names corresponding to columns of counts array. Required when counts is a numpy array.

  • **kwargs – Additional engine-specific parameters.

Return type:

DataFrame