GSVA analysis between Clusters
Entering edit mode
2.1 years ago
David_emir ▴ 430

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,

Differences in pathway activities scored per cell by GSVA between the different fibroblast clusters. Shown are t values from a linear model, corrected for the patient of origin.

Thanks a lot for your Support, Stay safe!

Regards, Dave

GSVA Single cell seurat • 2.7k views
Entering edit mode
2.1 years ago
khorms ▴ 210

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


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