dilimap.pp.deseq2

dilimap.pp.deseq2(adata, pert_name_col, other_pert_cols=(), condition_cols=(), dmso_pert_name='DMSO', dask_client=None, tempdir_prefix=None, **kwargs)

Runs DESeq2 for differential expression signatures across perturbations.

This function executes the DESeq2 model to compare gene expression changes across different perturbations. It supports parallel processing using Dask.

Parameters:

  • adata (AnnData) – An AnnData object containing gene expression count data.

  • pert_name_col (str) – Column name in adata.obs specifying the perturbation (e.g., drug).

  • other_pert_cols (tuple of str) – Additional columns to consider (e.g., dose).

  • condition_cols (tuple of str) – Columns specifying experimental conditions.

  • dmso_pert_name (str) – The name of the negative control perturbation (e.g., DMSO).

  • dask_client (dask.distributed.Client) – A Dask client for parallel processing.

  • tempdir_prefix (str) – Prefix for temporary directories used during processing.

  • **kwargs – Additional arguments passed to the DESeq2 model function.

Returns:

A new AnnData object containing the DESeq2 results

  • pvalue, FDR and LFC (log2 fold change) in layers for each gene and perturbation.

  • obs with summarized perturbation metadata.