I have a question on the best practice for testing DEG using 10X data where we also have biological replicates between our conditions. What is the recommended way to account for this replication? If this has already been addressed elsewhere please point me to it! Thanks

There is some commentary on this in the book.

There is also the muscat package, which mainly differs from scran::pseudoBulkDGE in that the former expects the pseudo-bulk SE to contain different assays for each cell type/cluster while the latter expects the pseudo-bulk SE to contain a single assay with all cell types/clusters.