DE

class brisc.DE(source=None, /, *, table, voom_weights=None, voom_plot_data=None)

Differential expression results returned by Pseudobulk.DE().

Parameters:

• source : str | Path | None

• table : pl.DataFrame

• voom_weights : dict[str, pl.DataFrame] | None

• voom_plot_data : dict[str, pl.DataFrame] | None

I/O

DE.__init__	Initialize the DE object.
DE.save	Save a DE object to directory (which must not exist unless overwrite=True, and will be created) with the table at table.parquet.

Properties

DE.groups

a dictionary mapping cell type names to group names used by voomByGroup for that cell type, or None if voomByGroup was not used for that cell type.

Analysis

DE.get_hits	Get all (or the top) differentially expressed genes.
DE.get_num_hits	Get the number of differentially expressed genes in each cell type.
DE.plot_voom	Generate a voom plot for a cell type that differential expression was calculated for.
DE.plot_volcano	Generate a volcano plot of the DE hits, with negative log p-values (or another significance_column) on the y-axis plotted against log fold changes on the x-axis.