i am working with two sc-rna seq data. pre and post treatment. i first performed cell ranger count to obtain the filtered gene matrix files. then loaded it into seurat and performed normalization, scaling. Then identified clusters and its markers, annotated the cells using singleR tool separately for pre and post dataset. Now i want to compare the genes of one cluster-tcell cluster of both the data, for differential expressed genes. What to do ? Is my working till now,right?
As mentioned, i am not sure if i can perform differential expression for the t cell clusters of the two data, because the cluster information is not in count format rather it has p_value details.