I would like to test the
zinbwave package with my data, but not sure, what is the correct procedure for that.
We have several experimental conditions/timepoints sequenced by 10x and would like to compare them against each other. They are all in duplicates (two biological replicates for each TP).
How would one go ahead with duplicated? Do I need to merge the two biological replicates into one sample and then continue to work with it as one, or is there a way to classify them as belonging to the same condition, when doing the DE analysis?
Would it be better first to use Seurat to integrate each two conditions (so four samples) to prevent possible batch effects into one integratedData object, keeping the project.Ident in place so they can be compared?