How to use SingleR for annotating single-cell transcriptomics dataset with our own custom made bulk RNA data?
1
0
Entering edit mode
2.5 years ago
A248 ▴ 10

Is this possible on the latest SingleR release version (3.10)? It looks like its fairly easy to use pre-existing Bulk RNA signatures from the built-in references, but when the bulk RNA data is generated by ourselves, is this possible?

Thanks in advance!

single cell sequencing annotation singleR • 1.1k views
ADD COMMENT
0
Entering edit mode

Hi @A248. Were you able to successfully use Bulk RNASeq data for labeling scRNASeq data?

ADD REPLY
1
Entering edit mode
2.5 years ago

Sure, you just have to feed it the counts (ref argument) and a vector of labels (labels argument) corresponding to each sample. Reading ?SingleR should explain pretty clearly.

ADD COMMENT

Login before adding your answer.

Traffic: 2062 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6