Database for mice - Githubissues

Coolgenome / iTALK

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Database for mice #7

Open Key0624 opened 5 years ago

Key0624 commented 5 years ago

Hi, I honestly think that your work very impressive, but I met a problem when I use iTALK R package to process the scRNA-seq data from mice(Mus musculus). It seems that my data can't match the ligand-receptor pairs in your current database probably because the gene names are different between human(upper-case) and mice(lower-case except the first letter). I'm wondering how to solve this problem and looking forward to your reply.

Yale73 commented 4 years ago

@Key0624 Have you solve this problem or not? I find I also can't get the matched ligand-receptor pairs.

Thanks Yale

ywang65 commented 4 years ago

Sorry for the late reply. My computer went wrong for a while. This database is based on gene pairs for human. If you want to use it for mice data, you need to use other tools to transfer Ligand.ApprovedSymbol and Receptor.ApprovedSymbol into mice genes

zehualilab commented 4 years ago

library(Hmisc) MouseSymbol <- rownames(counts_matrix) HumanSymbol <- Capitalize(tolower(MouseSymbol)) rownames(counts_matrix) <- HumanSymbol

You could also use nichenetr::convert_mouse_to_human_symbols()