I have a single cell RNA-seq data form 10X genomics. I want to perform pathway analysis of top 50 genes of each cluster on the the basis of DE. These clusters represent cells with similar expression of genes. So in pathway analysis of these top 50 genes I want to identify what possible type of cells they may be. There are several types of pathway analysis- like IPA, Enrichr, David and so on. Any suggestion which tool will be the the best to at least suggest that clustered cells are of a particular cell type and has a specific pathways enriched in them. e.g if Stem cell pathway is enriched we may say that these are pluripotent cells. Any suggestion?
If you only take the top 50 genes, you might be missing a lot of information. Also, depending on what the other clusters are, the differentially expressed genes will change. You can take the average expression of all genes for each cluster and then use a cell type deconvolution tool. Check this previous discussion where there are a few great suggestions: Deconvolution Methods on RNA-Seq Data (Mixed cell types)