omicverse.single.DEG

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omicverse.single.DEG#

class omicverse.single.DEG(adata, condition, ctrl_group, test_group, method='wilcoxon', use_raw=None)[source]#

Differential gene-expression testing wrapper for single-cell datasets.

Parameters:

  • adata (AnnData) – Input single-cell AnnData.

  • condition (str) – Condition column in adata.obs.

  • ctrl_group (str) – Control-group label.

  • test_group (str) – Test-group label.

  • method (str, default='wilcoxon') – DEG method name.

  • use_raw (bool or None, default=None) – Whether to use adata.raw as expression matrix.

__init__(adata, condition, ctrl_group, test_group, method='wilcoxon', use_raw=None)[source]#

Initialize differential expression analysis.

Parameters:

  • adata (AnnData) – Single-cell AnnData object.

  • condition (str) – Obs column containing condition labels.

  • ctrl_group (str) – Control condition label.

  • test_group (str) – Test condition label.

  • method (str, default='wilcoxon') – DEG method: 'wilcoxon', 't-test', or 'memento-de'.

  • use_raw (bool or None, default=None) – Whether to use adata.raw as expression matrix. If None, auto-detects based on availability.

Return type:

None

Methods

__init__(adata, condition, ctrl_group, ...)

Initialize differential expression analysis.

get_results()

Get DEG result table.

run(celltype_key[, celltype_group, max_cells])

Run differential expression testing.
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