Meeta Mistry comments

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                                            Meeta Mistry

scores and p-values

Thanks @AliciaSchep . So what you are saying is that p-values are not derived for each individual site? In that case, I wouldn't need the p-values since I was assuming...

Change to log2FC shrinkage to apeglm following advice in Mike

adding a note in lesson for now, will address for next iteration of workshop

Change to log2FC shrinkage to apeglm following advice in Mike

added a note to address this and https://github.com/hbctraining/DGE_workshop_salmon/issues/41 in the online materials

coef vs contrast?

have a note mentioning coef and methods for apeglm when running lfcshrink()

coef vs contrast?

added a note into the online materials

Update workflow image with log2FC shrinkage after DE testing

updated in the online materials

include greylisting in DiffBind lesson

This is now an option in DiffBind, so we can explain it here

add a library preparation slide deck?

Remove library prep materials from the RNA-seq intro markdown

Pseudobulk functionality within Seurat

Thanks @pipes82 :) We are working on creating a new module with this new functionality!

Update workflow for planning successful RNA-seq

count modeling and hypothesis testing markdown needs a change