spatial registration of psychENCODE Data

LieberInstitute / spatialDLPFC

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

http://research.libd.org/spatialDLPFC/

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spatial registration of psychENCODE Data #122

Closed abspangler13 closed 2 years ago

abspangler13 commented 2 years ago

/dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC/raw-data/psychENCODE/version2

[ ] problem with DupCor() getting stuck. probably because of covariates.
[ ] remove covariates all together

abspangler13 commented 2 years ago

The SZBD dataset gets stuck at duplicateCorrelation() in the enrichment analysis. However, I did successfully make the pseudobulked object which is saved.

lcolladotor commented 2 years ago

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

lahuuki commented 2 years ago

Will we want to save the data (correlation and/or layer annotations) to an excel sheet for individual csv files?