Batch correction for Seurat objects

[danafd]

Hi, Is there an available script for preparing Seurat data for batch preprosessing of count data in jupyter notebook?

I am running the cNMF code from R and would like to see if there is a batch effect in my data, would this be possible?

[dylkot]

Hey @danafd, eventually this will be written for use on the command line but it isn't ready quite yet. For now I would convert the R data to Python like what is shown here and then follow the instructions for Python. Sorry, hopefully we will get the fully command line version of batch correction ready soon.

[danafd]

Will give it a try. Thanks!