Question

SingleR Label.Ont

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saeed.khalili • 0

@7bbacdad

Last seen 8 months ago

Canada

Hi, I am new in using SingleR to annotate Visium RNA Seq data on Human Skin and wondering if there is a way to convert label.ont (i.e. CL:0000840) into gene name. Can you please advise? Thanks.

Cheers, Saeed

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

SingleR • 19k views

ADD COMMENT • link updated 2 days ago by marusya • 0 • written 9 months ago by saeed.khalili • 0

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score 0 · Answer 1 · 2023-09-15

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ATpoint ★ 4.2k

@atpoint-13662

Last seen 57 minutes ago

Germany

SingleR returns per-cell or per-cluster labels, not genes. The CL:0000840 is a myeloid label, see https://bioconductor.org/packages/release/data/experiment/vignettes/celldex/inst/doc/userguide.html to get the HPCA table that allows translation from ont to actual human-readable label.