Thank you for your interest in the package.
Generally, I'd combine all samples across batches by simply merging. If common cell types separate due to batch effect, merge samples per batch and try an integration approach as outline here.
If this does not answer your question try looking in the Seurat issues, as this is really a workflow specific question outside the scope of the issue tracker for this package.
Best, Christoph
Thank you for your interest in the package. Generally, I'd combine all samples across batches by simply merging. If common cell types separate due to batch effect, merge samples per batch and try an integration approach as outline here. If this does not answer your question try looking in the Seurat issues, as this is really a workflow specific question outside the scope of the issue tracker for this package. Best, Christoph
Originally posted by @ChristophH in https://github.com/satijalab/sctransform/issues/32#issuecomment-517235017