Generate a fraction of immune cell between two condition from single cell RNAseq

Question

[synat.keam]

Dear Fellows,

Do you know any tutorial to generate fractions of immune cells from total cells as in figure (e) of attached image between two condition. Could not find any script to do that. Really appreciate your help.

Regards

[bk11]

Hey, what is your analysis tool? You can split your single cell dataset into immune, non-immune or any other compartments fairly easily using basic functions in both R and Python. Please consider investing your time learning basics.

Answer 1

[Haci]

If you have reference data sets (basically annotated single cell data), you can use SingleR. Moreover, CellTypist has built-in references and seems to be doing a good job in terms of immune cell types.

[synat.keam]

Thanks, Haci. Really appreciated your response. I reviewed the CellTypist briefly and seems a bit confusing. Goal is I have numbers of clusters from Seurat and Harmony integration and have differentially expressed genes from each cluster. Therefore, I am looking whether a list of genes that have increased logfold changes represents what cell types. Does cell typist accept a list of gene and predict the cell type? Sorry for asking, but I think you may be able to explain me briefly. I will read further. Thanks,

Answer 2

[Radu Tanasa]

You can annotate your cells based on your UMAP clusters. Usually, this is done at multiple resolutions. Once you have your cells properly annotated, you can use tools like scCODA (python) to perform compositional analysis.