8 Tips

Compiled: 2025-05-08 Written by Jiaying Zeng and Daihan Ji

Here are some helpful tips for you to use SingleCellMQC more smoothly.

8.1 Progress updates

Turning on the global progress update report feature before your analysis is suggested, so that you could keep better track of the whole QC progress.

library(progressr)
handlers(global = TRUE)

8.2 Future parallel

  • Future parallel global memory setting

When you initiate the work by future parallel, the default global memory limit is 500MB, which is often insufficient, so it’s recommended to set it to 1GB or higher. For example, you can set global memory limit to 1GB (1024 MB * 1024 KB/MB * 1024 B/KB).

library(future)
options(future.globals.maxSize = 1024 * 1024 * 1024)
  • How to use parallelization
library(future)
# change the current plan to access parallelization
plan("multiprocess", workers = 4)

# task example: e.g. scDblFinder doublet detction
pbmc<- RunDbt_scDblFinder(pbmc, split.by = "orig.ident", add.Seurat=T, do.topscore=T)

# change the the current plan to sequential
plan("sequential")

  • Functions supporting

  • Read data (v0.6.0+): Read10XData, Read10XH5Data

  • Doublet detection (v0.6.0+): RunDbt_hybrid, RunDbt_bcds, RunDbt_cxds, RunDbt_scDblFinder, RunDbt_DoubletFinder, RunDbt_ADT