Hi, I'm using SingleR for annotating pbmc data(pbmc4k). I am using Tabula sapiens immune dataset as a reference dataset which has dim (58870, 264824). Currently I am using 24 CPU cores by setting BPPARAM=MulticoreParam(24). When I use singleR to get predictions it hangs and there are no results till a few hours. Also it takes long to retrieve elements manually in Tabula Sapiens SingleCellExperiment class. What changes in configuration can I make to run it faster and can I see the status of singleR predictions (like how many cells are annotated) ?
Please post issues in https://github.com/LTLA/SingleR
Hi, I'm using SingleR for annotating pbmc data(pbmc4k). I am using Tabula sapiens immune dataset as a reference dataset which has dim (58870, 264824). Currently I am using 24 CPU cores by setting BPPARAM=MulticoreParam(24). When I use singleR to get predictions it hangs and there are no results till a few hours. Also it takes long to retrieve elements manually in Tabula Sapiens SingleCellExperiment class. What changes in configuration can I make to run it faster and can I see the status of singleR predictions (like how many cells are annotated) ?