Annotating single cell data automatically
Entering edit mode
5 weeks ago
Gerard • 0

Hello !

When using seurat to get an object with different clusters of a specific cell type, let's say t cells, I'm looking for ways to automatically annotate them, so it can tell me which one are cd4, which are cd8, which are memory etc.

I've been told to use azimuth, however from seurat I didn't manage to get the appropriate input data. Same for the SingleR package, which requires a numeric matrix of single-cell expression values where rows are genes and columns are cells.

In either case, I struggle to get the appropriate data from my seurat object to run these.

Can anybody help ?

Thank you

single-cell • 260 views
Entering edit mode
3 days ago
Francesco ▴ 10
  • In order to run Azimuth:
AzimuthClusters <- RunAzimuth(seurat_obj, reference = "pbmcref")
  • singleR

surveyReferences() # it lists all available references

ref <- fetchReference("monaco_immune", "2024-02-26")
seurat_dex <- as.SingleCellExperiment(seurat_obj)
predMainMonaco <- SingleR(test = seurat_dex, ref = ref, labels = ref$label.main, BPPARAM = BiocParallel::SerialParam())

Hope it helps


Login before adding your answer.

Traffic: 1190 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6