davislaboratory / scdecaf Goto Github PK

as per mention in #2

Hello, I have a question regarding the input data. As mentioned in the help document, the input "data" for scDECAF() is a numeric matrix where rows are genes and columns are cells or samples. I would like to ask, typically, what kind of columns would you like to suggest to use when applying scDECAF? Do you suggest to use different cells, or biologically repeated samples, or the same cells / samples but at different time points? It would be highly appreciated if you could give me some simple examples. Thanks a lot :)

Hi! I'm working on a single-cell RNA project that compares single-cell transcriptomic data of embryonic and adult mouse colons to identify embryonic-specific gene signatures and use these genes to score colon cancer single-cell data. I find the scDECAF algorithm is suitable for this project.

I have some problems understanding the inputs to the algorithm in the Quick Start part.

• For the variable x, can I put the SingleCellExperiment object?
• I don't know the meaning of geneset and the HM_geneset. Does the HM_geneset represent the human geneset that can be downloaded online? How about the mouse geneset?

What I have now is the gene signature, a vector of gene ids, like "ENSMUSG00000031957" "ENSMUSG00000069893" "ENSMUSG00000055827"...; the data I want to score: a SingleCellExperiment object; a list of highly variable genes (hvg).

Very much appreciate it if you could give me some instructions! Thanks!