msmu.tl.run_de

Run Differential Expression Analysis (DEA) between two groups in a MuData object.

Parameters:

Name	Type	Description	Default
mdata	MuData	MuData object containing the data.	required
modality	str	Modality name within the MuData to analyze.	required
category	str	Observation category to define groups.	required
ctrl	str	Name of the control group.	required
expr	str | None	Name of the experimental group. If None, all other groups are used.	None
layer	str | None	Layer to use for quantification aggregation. If None, the default layer (.X) will be used. Defaults to None.	None
stat_method	Literal['welch', 'student', 'wilcoxon']	Statistical test to use ("welch", "student", "wilcoxon").	'welch'
measure	Literal['median', 'mean']	Measure of central tendency to use ("median" or "mean") for fold-change.	'median'
n_resamples	int | None	Number of resamples for permutation test. If None, no permutation test is performed.	1000
fdr	bool | Literal['empirical', 'bh']	Method for multiple test correction ("empirical", "bh", or False).	'empirical'
log_transformed	bool	If True, data is assumed to be log-transformed. Defaults to True.	True
_force_resample	bool	If True, forces resampling even if the number of resamples exceeds the number of combinations.	False

Returns:

Type	Description
DeaResult	DeaResult containing DE analysis results.