re-make pseudobulked objects

LieberInstitute / Visium_SPG_AD

Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.

https://research.libd.org/Visium_SPG_AD

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re-make pseudobulked objects #58

Closed abspangler13 closed 2 years ago

abspangler13 commented 2 years ago

resolve this: https://jhu-genomics.slack.com/archives/CR9NYA0BF/p1652035798464949. need to go back change the FilterByExpr use in pseudobulking code. look at latest visium_IF_AD. switch column names from low to high so it's self-explanatory. make sure to use group argument in order to keep more genes. need to make different pseudobulked objects for each differential expression analysis. group by region for region DE analysis.

lcolladotor commented 2 years ago

I think that you meant to do this at https://github.com/LieberInstitute/spatialDLPFC/issues, right?

abspangler13 commented 2 years ago

Yes oops!