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hbctraining / scRNA-seq_online

https://hbctraining.github.io/scRNA-seq_online/.
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Simpler way to go from seurat object to DESeq2 analysis? #54

Closed learning-MD closed 2 years ago

learning-MD commented 3 years ago

Thanks for the wonderful tutorial! This, in combination with Seurat vignettes, has been incredibly helpful.

One question I had, as a primary wet lab worker who is learning more R and the computational side: Is there a simpler way to get from the merged Seurat object (e.g. 8 total samples, 4 control and 4 disease) to creating the DESeq2 object? As someone still self-teaching R, some of the pseudobulk tutorial (https://github.com/hbctraining/scRNA-seq_online/blob/master/lessons/pseudobulk_DESeq2_scrnaseq.md) assumes a better grasp of base R than I currently have.

Any guidance would be much appreciated! Thanks again for creating this fantastic tutorial for people like me!

mistrm82 commented 2 years ago

Hi @learning-MD ,

Unfortuntaley, we have not yet encountered any packages/functions that have been created to directly create pseudobulk matrices for each cluster. It is alot of code, but if you go step by step and examine each object as your create it, that can be more intuitive.