Preform Deconvolution with Bisque - Githubissues

LieberInstitute / zandiHyde_bipolar_rnaseq

RNA-seq analysis for psychENCODE R01

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Preform Deconvolution with Bisque #7

Closed lahuuki closed 3 years ago

lahuuki commented 3 years ago

[x] Check all cellType markers are expressed
[x] Run Bisque
[x] Composition Bar plot
[x] Box plot by Dx
[x] prop vs. qSV values: grid and tiles
[x] t-stats with 0.05 & 0.01 FDR cut offs
[x] top tables for DE with prop terms in model

lahuuki commented 3 years ago

Export top table - excel sheet with separate sheets for each region. Create separate files for prop and ilr models.

lcolladotor commented 3 years ago

For using xlsx, you need to request some more mem for Java before opening R like at https://github.com/LieberInstitute/brainseq_phase2/blob/e1a67fe8900ffcc637ad7f405b620dc15a93d4af/supp_tabs/twas_supp.R#L4-L5