Question1:

SingleR for integrated scRNA-seq analysis 注释该用哪个文件？

I am using SingleR to identify cell type for each cluster and I am wondering if I need to set DefaultAssay as "RNA" or "integrated". I tried both, but they gave me slightly different results for cell type identification.

Should I keep DefaultAssay as "RNA" or "integrated"?

Any thoughts and advice are greatly appreciated. Thank you.

The assay should be RNA, since SingleR expects expression values.

https://www.biostars.org/p/442514/

2.英文教程

http://127.0.0.1:18254/library/SingleR/doc/SingleR.html

中文教程

学习对scRNA-seq数据注释的R包SingleR
https://www.jianshu.com/p/559399aef148

3. 参数

https://rdrr.io/bioc/SingleR/man/SingleR.html

4 安装

https://www.bioconductor.org/packages/release/bioc/html/SingleR.html