Entry level Bioinformatician here. I am trying to map my single cell data with standard annotation file or assign my Seurat cluster to cell types. I have used the singleR and celldex package to map it but my problem is the single cell only consist of endothelial cells. I haven't found paper that only consist of rats endothelial cells. The single cell data is for rats. I am stuck. What is the best thing that could be done here?
It seems like you can annotate all your cells as endothelial cells, problem solved ;) But seriously, not clear what your expected cell types are (subtypes of endothelial cells perhaps) or the tissue type. If you can't find a suitable reference dataset for the reference mapping approach, then you can always resort to the 'old fashioned' way of unsupervised clustering (e.g leiden) plus checking marker gene expression to annotate the clusters.
An alternative approach, could be finding a suitable human/mouse reference and then converting the gene ids to rat (ideally via 1:1 ortholog mapping) but this could get messy, so I suggest the former simpler way, at least as a starting point