GSVA analysis between Clusters

Question

[David_emir]

Hi All,

I am currently working on Tumor Normal Single-cell dataset (10X droplets) using Seurat protocol. I am interested in finding the differences in pathway activities scored per cell by GSVA(Gene set variation analysis) between the different clusters of a cell type (epithelial subtype). one PAPER speaks about GSVA analysis in clusters.

My question how can I do GSVA for my 22 clusters? please let me know if you guys have a particular protocol to be followed in this case or any strategies to be employed. I wanted to generate a heatmap like the following,

Thanks a lot for your Support, Stay safe!

Regards, Dave

Answer 1

[khorms]

I am not sure about Seurat but another very popular single cell analysis framework Scanpy allows you do perform GSVA analysis with tools like diffxpy