What is the best integration package for large single cell RNA sequencing dataset.

Question

[Andy]

Hello everyone,

I was wondering which integration package is recommended for analyzing large single-cell RNA sequencing data, specifically for datasets with over 100,000 cells.

Best regards, Andy

Answer 1

[rpolicastro]

I've found scVI to perform the best over a diversity of datasets, while also consuming very little memory out to 1m+ cells.

[archanaverma433]

Hi, I also have 3,00,000 cells with different subgroup data from different Batches and i want to integrate these data. Is there any R package for integration? I have used seurat v4 integration method and it works well with less than 1,00,000 cells but I think it is not best for more than million cells.

Thank you!

[rpolicastro]

scVI really is your best option. Seruatv5 has a wrapper for it, or you can use reticulate to call it from R.