Cell type annotation in Sc-RNA Seq data

Question

[Maria17]

Greetings,

I have single-cell sequencing data from three different Patients(hepatocellular cancer). I'm trying to annotate the cell types for each cluster using SingleR and Celldex libraries.

I have Gene Ensemble Ids in Seurat object or Sce object. I don't know how to modify hpca.se to have ensemble ID instead of gene names.

Any recommendation or other tools for cell-type annotation would be appreciated.

Answer 1

[Friederike]

Try setting ensembl=TRUE when loading the hpca.se data set (see the celldex vignette). This way the gene names should be returned in ENSEMBL format.