Filter based on expression or custom clusters


I have a large single cell population (+100k cells) that are incredibly heterogenous. I’d ideally like to filter early on to select different populations out of the whole based on three to five marker genes. I’ve also thought about clustering based on these markers, but I’m unsure how to go about either of these methods.

I’ve tried: adata[(adata[:,‘GFP’].X>0).flatten(), : ] - but I receive an error that ‘flatten’ is not found. Similarly, when I attempt to cluster based on markers that feed in, I end up with 50+ clusters, and a majority of the cells being located in one central cluster.

I know neither of these methods are the exact best way to analyze data, but this is more for a preliminary check on our end before proceeded with a new single cell kit.