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LieberInstitute / zandiHyde_bipolar_rnaseq

RNA-seq analysis for psychENCODE R01
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Test for DE in marker genes used for deconvolution #14

Closed lahuuki closed 1 year ago

lahuuki commented 2 years ago

Responding to concerns from reviewer 1, test for differential expression of genes between regions (sACC vs. Amyg) in the snRNA-seq for the set of marker genes we used.

lcolladotor commented 2 years ago

Check sections 14.3.2 and 14.3.3 from OSCA at https://bioconductor.org/books/release/OSCA/multi-sample-comparisons.html#performing-the-de-analysis.

Basically, we can use pseudoBulkDGE() on an SCE object with the sACC and AMY data to test for DE between brain region across each broad cell type.

lcolladotor commented 2 years ago

We can likely close this issue, right? Now that the paper has been published.