Single cell RNAseq

[ggonnella]

Can it be used with scRNA-seq data, eg. from Seurat? I was thinking of pseudobulk comparison of cell types in two conditions.

[egeulgen]

thanks for your interest @ggonnella. You can use pathfindR with any input data containing Gene symbols and associated significance values. For scRNAseq, you can first run Seurat::FindMarkers for finding differentially expressed genes and use the result as input for active-subnetwork search + enrichment analysis via pathfindR.