Batch correction for Seurat objects

dylkot / cNMF

Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

MIT License

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Batch correction for Seurat objects #91

Open danafd opened 1 week ago

danafd commented 1 week ago

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 commented 1 week ago

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 commented 1 week ago

Will give it a try. Thanks!