diff --git a/pegasus/tools/pseudobulk.py b/pegasus/tools/pseudobulk.py index 75e8493..e50a940 100644 --- a/pegasus/tools/pseudobulk.py +++ b/pegasus/tools/pseudobulk.py @@ -30,12 +30,12 @@ def get_pseudobulk_count(X, df, attr, bulk_list): @timer(logger=logger) def pseudobulk( - data: MultimodalData, + data: Union[MultimodalData, UnimodalData], groupby: str, attrs: Optional[Union[List[str], str]] = None, mat_key: str = "counts", condition: Optional[str] = None, -) -> UnimodalData: +) -> MultimodalData: """Generate Pseudo-bulk count matrices. Parameters @@ -157,9 +157,7 @@ def deseq2( compute_all: bool = False, n_jobs: int = -1, ) -> None: - """Perform Differential Expression (DE) Analysis using DESeq2 on pseduobulk data. This function calls R package DESeq2, requiring DESeq2 in R installed. - - DE analysis will be performed on all pseudo-bulk matrices in pseudobulk. + """Perform Differential Expression (DE) Analysis using DESeq2 on pseduobulk data. Parameters ----------