Often we provide to these tools AnnData files where the index is the gene_id and the gene symbols are in another field of the var. However, gene set tools will often rely on the gene symbol, so we need to indicate where the gene symbol is in our anndata and make use of this information so that the tool runs against those gene symbols. This is done in decoupler AUCell here:
Often we provide to these tools AnnData files where the index is the gene_id and the gene symbols are in another field of the var. However, gene set tools will often rely on the gene symbol, so we need to indicate where the gene symbol is in our anndata and make use of this information so that the tool runs against those gene symbols. This is done in decoupler AUCell here:
https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/blob/main/tools/tertiary-analysis/decoupler/decoupler_aucell_score.py#L117