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
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