Save normalized counts from pseudobulk method(s)

[lianov]

Hello,

Thank you for developing this tool. I have a question:

Are there currently any plans on providing an additional parameter that we can pass to to run_de to output normalized counts from the methods implemented for pseudobulk DE? For example, around https://github.com/neurorestore/Libra/blob/main/R/pseudobulk_de.R#L99, there could be an additional feature to also save the normalized counts from EdgeR; same for DESeq2 etc.

While to_pseudobulk provides pseudobulk counts, these are further normalized within each tool and thus would be a useful set of outputs for plotting purposes of pseudobulk counts of specific genes (e.g.: https://github.com/hbctraining/scRNA-seq_online/blob/master/lessons/pseudobulk_DESeq2_scrnaseq.md#scatterplot-of-normalized-expression-of-top-20-most-significant-genes).

Wanted to check-in if there are any plans on adding this. Thank you!

[neurorestore]

Yes we have this on the list of features to add - thanks for pointing it out! If you already implemented it please feel free to send a PR.

[lianov]

Thanks for the update! And no, I do not have this implemented yet as we have just come across this resource. Looking forward to it! (and if I do implement this ahead, will be sure to send PR).