Cell type annotation in Sc-RNA Seq data
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.
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Friederike
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Maria17 •
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Maria17 •
1 answer
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.
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