Closed abspangler13 closed 1 year ago
The SZBD dataset gets stuck at duplicateCorrelation() in the enrichment analysis. However, I did successfully make the pseudobulked object which is saved.
From https://www.synapse.org/#!Synapse:syn30043916, it looks like we need to redo this with the subclass
column, not the anno
column. That will involve changing things like https://github.com/LieberInstitute/spatialDLPFC/blob/5820293a9e6611a7ab9f33265c00bfa5da014fa1/code/analysis/14_spatial_registration_PEC/01_pseudobulk_DevBrain.R#L27
Will we want to save the data (correlation and/or layer annotations) to an excel sheet for individual csv files?
/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/psychENCODE/version2