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This repository has been archived by the owner on Jan 24, 2024. It is now read-only.
Hope you are doing well. I was wondering if you could help me update CellChatDB by adding ligand-receptor pairs using data from OmniPath?
OmniPath contains a remarkably high number of, manually curated, high quality interactions that will increase the quality of CellChatDB significantly. I have attached the data here below.
However, I just cannot seem to implement it, probably because it is outdated and not compatible with the current version of OmniPath. After running the function it always gives me the same output as CellChatDB, nothing gets updated.
Can you please help me add all the interactions from Omnipath to CellChatDB?
Adding OmniPath will not only increase the range of interactions that CellChat can detect but this will immensely useful to the whole research community!
The text was updated successfully, but these errors were encountered:
@superman2412 Have you checked https://github.com/saezlab/liana? I think the convert function they provided could solve your issue. If you still have some issues, you can directly contact the first author of liana
@sqjin Thank you for your response. Unfortunately, that facility is not available in Omnipath / LIANA at this stage. More information can be obtained by the developers of Omnipath / LIANA on the following link.
Hello again Dr. Jin @sqjin!
Hope you are doing well. I was wondering if you could help me update CellChatDB by adding ligand-receptor pairs using data from OmniPath?
OmniPath contains a remarkably high number of, manually curated, high quality interactions that will increase the quality of CellChatDB significantly. I have attached the data here below.
all_interactions.csv
I did come across a function to be able to add Omnipath data to CellChat using the function in this post: https://github.com/saezlab/OmnipathR/issues/28#issuecomment-830045576.
The function is:
`#' Helper Function to Format to CellChatDB
#' @param ccDB Inbuilt cellchatDB object
#' @param op_resource omnipath resource
#' @param exclude_anns annotations to exclude
#' @import tibble
#' @importFrom magrittr %>%
#' @importFrom stringr str_glue str_detect str_replace str_replace_all
cellchat_formatDB <- function(ccDB, op_resource, exclude_anns){
# get complexes and interactions from omnipath
complex_interactions <- op_resource %>%
select(
"genesymbol_intercell_source" = target,
"genesymbol_intercell_target" = source,
"ligand" = source_genesymbol,
"receptor" = target_genesymbol,
"evidence" = sources,
category_intercell_source,
category_intercell_target,
is_directed,
is_stimulation,
is_inhibition
) %>%
unite("annotation",
c(category_intercell_source, category_intercell_target),
sep="-") %>%
unite("interaction_name", c(ligand, receptor), remove = FALSE) %>%
mutate(pathway_name = "",
agonist = "",
antagonist = "",
co_A_receptor = "",
co_I_receptor = "") %>%
mutate_at(vars(everything()), ~ replace(., is.na(.), ""))
However, I just cannot seem to implement it, probably because it is outdated and not compatible with the current version of OmniPath. After running the function it always gives me the same output as CellChatDB, nothing gets updated.
Can you please help me add all the interactions from Omnipath to CellChatDB?
Adding OmniPath will not only increase the range of interactions that CellChat can detect but this will immensely useful to the whole research community!
The text was updated successfully, but these errors were encountered: