search

satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
Other
2.26k stars 907 forks source link

Gene-gene correlation/de novo identification of co-regulated gene modules #1622

Closed ws2260 closed 5 years ago

ws2260 commented 5 years ago

Hi,

I'm trying to find a way to look check modules of co-expressed genes. I'm aware that there is the AddModuleScore function in Seurat but is there a way to identify gene modules de novo before using those modules and applying the module scores for the clusters.

I suppose one way to visualize this is a gene-gene correlation matrix heatmap of top variable genes to see the modules of co-expressed genes. Is there a proper way/an example I can follow?

Thanks!

satijalab commented 5 years ago

We often use the DimHeatmap function for the purpose of visualizing correlated sets of genes, as you can see at https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html. We find this very effective, but we have also seen instances where other groups have run WGCNA to find modules in single-cell data (though this is not native in Seurat).