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hbctraining / scRNA-seq_online

https://hbctraining.github.io/scRNA-seq_online/.
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Pseudobulk functionality within Seurat #116

Open pipes82 opened 5 months ago

pipes82 commented 5 months ago

Hi All! I wasn't sure if you had seen that Seurat now has a function for aggregating to the sample level for pseudobulk DE analysis. Using a few functions as detailed at the end of this Seurat vignette: https://satijalab.org/seurat/articles/parsebio_sketch_integration.

The Seurat developers perform most of our whole pseudobulk lesson in a few functions. I would still QC a bit more than they do prior to performing the DE - filter samples based on minimal # of cells for each individual cell type being tested (~20 cells?) and/or filter genes based on a minimum number of samples and cells for which a gene must have reads. However, it could really reduce the pain of performing the pseudobulk analysis. Caveat: I haven't tested it out yet though.

mistrm82 commented 5 months ago

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