nichenet_signaling_network_omnipath: Builds signaling network for NicheNet using OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

Builds signaling network for NicheNet using OmniPath

Description

Retrieves network prior knowledge from OmniPath and provides it in a format suitable for NicheNet. This method never downloads the 'ligrecextra' dataset because the ligand-receptor interactions are supposed to come from nichenet_lr_network_omnipath.

Usage

nichenet_signaling_network_omnipath(min_curation_effort = 0, ...)

Arguments

min_curation_effort	Lower threshold for curation effort
...	Passed to import_post_translational_interactions

Value

A network data frame (tibble) with signaling interactions suitable for use with NicheNet.

See Also

• nichenet_signaling_network

Examples

# use interactions with at least 2 evidences (reference or database)
op_signaling_network <- nichenet_signaling_network_omnipath(
    min_curation_effort = 2
)

saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.