Question: Is there a comprehensive gene list available that will enable me to annotate clusters to their respective cell types?
Answer: 10x Genomics does not provide official guidelines on annotating cell types. However, the information below might help.
For PBMCs, you could use the 10 marker genes listed in the AMLBloodCell.csv. That is used in our tutorial on annotating cell types using Loupe Browser.
You could also use the community-developed resources for cell type annotation. Please see this article below for some useful web resources:
- Analysis Guide Introduction: Web resources for cell type annotation.
In addition, there are additional community-developed packages for cell type annotation:
- Seurat's find.markers() function
- scmap: projection of single-cell RNA-seq data across data sets
- SingleR: reference-based single-cell RNA-seq annotation
- CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing
Please note that this is not a comprehensive list. Cell type annotation is an active area of research, and you may find more updated information based on your search.
Disclaimer: This article and code-snippet are provided for instructional purposes only. 10x Genomics does not support or guarantee the listed tools or code. Please contact the respective authors of each article/tool for more information.