Cell type annotation in Sc-RNA Seq data
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Entering edit mode
12 months ago
Maria17 • 0

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.

SingleR celldex cluster RNA-Seq R • 608 views
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Entering edit mode
12 months ago

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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