The scvi-tools tutorials datasets are pre filtered to eliminate doublets and low-quality cells and genes as detailed in the TotalVI paper. Can scvi-tools can be used to filter data sets?
I used Seurat in RStudio to clean up my data set to get rid of doublets, cells with < 200 genes, and cells with high mitochondrial and ribosomal RNA. I tried to convert the Seurat object into a h5ad file that I can open in Spyder (Python 3.8) but this file was not recognizable by scvi-tools.
What is the best way to filter the data easily (I find Seurat easy to use) and then use scvi-tools for analyses and figures?
##Export and use python tools
SaveH5Seurat(data, filename = “filtered-data.h5ad”)
Convert(“filtered-data.h5ad”, dest = “h5ad”)