get_curated_omni: Function to Generate the Curated (Default) LIANA resource

In saezlab/ligrec_decoupler: LIANA: a LIgand-receptor ANalysis frAmework

Function to Generate the Curated (Default) LIANA resource

Description

Function to Generate the Curated (Default) LIANA resource

Usage

get_curated_omni(
  curated_resources = c("CellPhoneDB", "CellChatDB", "ICELLNET", "connectomeDB2020",
    "CellTalkDB")
)

Arguments

curated_resources

the curated resources from which we wish to obtain interactions. By default, it includes interactions curated in the context of CCC from CellPhoneDB, CellChat, ICELLNET, connectomeDB, CellTalkDB, and SignaLink.

Details

Here, we define the curated resources as those that are defined as manually or expert curated in the context of cell-cell communication. Albeit, "Guide2Pharma", "HPMR", and "Kirouac2010" are also such resources the remainder of the resources used to generate Omnipath, use those as sources. Hence, we assume that the second round of manual curation done in subsequent, more recently published resources would already contain the high quality interactions of the aforementioned 3. We also omit Cellinker, as it results in a large mount of ambigous interactions, but one could consider adding it to the list of curated resources.

Value

a curated OmniPath resource formatted for LIANA

saezlab/ligrec_decoupler documentation built on Aug. 10, 2024, 8:56 a.m.