Hello,

I was reading on MiloR and wanted to use this tool to identify neighborhoods in my scRNA-seq dataset that correlate in abundance with a treament of interest. What I want to do in downstream analysis is to extract the barcodes of cells that belong to a neighborhood and perform a statistical comparison of gene expression with the rest cells in the same cluster. I understood that this is not possible since MiloR uses index cells to represent the neighborhoods, but the barcode identities of all cells that belong tothis neighborhood is not accessible. Am I right or is this information stored in the object, as well?

Thanks in advance!

Hi thkapell - Thanks for your question, and interest in Milo. We use the index cells as a way to a) define the neighbourhoods and b) anchor the neighbourhoods for intuitive visualisation. In reality we still keep a record of which cells are part of which nhoods in a nhood X cell indicator matrix that can be accessed with the nhoods() function. The columns names are the index cells in nhoodIndex().