get_de

besca.tl.dge.get_de(adata, mygroup, demethod='wilcoxon', topnr=5000, logfc=1, padj=0.05)

Get a table of significant DE genes at certain cutoffs Based on an AnnData object and an annotation category (e.g. louvain) runs scanpy’s rank_genes_groups using a specified method with specified cutoffs (nr. genes, logfc, padj) and returns a df with the results :param adata: AnnData object containing :type adata: AnnData :param mygroup: group for performing de, needs be in adata.obs :type mygroup: str :param demethod: one of ‘t-test’, ‘wilcoxon’, ‘t-test_overestim_var’, ‘logreg’ :type demethod: str :param topnr: the number of top genes in the DE analysis :type topnr: int :param padj: log fold-change cutoff :type padj: float :param logfc: adjusted p-value cutoff :type logfc: float

Returns:

a list of panda DataFrames of differentially expressed genes

Return type:

delist