nichenet_signaling_network_cpdb: Builds signaling network for NicheNet using ConsensusPathDB

In saezlab/OmnipathR: OmniPath web service client and more

Builds signaling network for NicheNet using ConsensusPathDB

Description

Builds signaling network prior knowledge using ConsensusPathDB (CPDB) data. Note, the interactions from CPDB are not directed and many of them comes from complex expansion. Find out more at http://cpdb.molgen.mpg.de/.

Usage

nichenet_signaling_network_cpdb(...)

Arguments

...	Passed to consensuspathdb_download.

Value

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

See Also

• nichenet_signaling_network

• consensuspathdb_download

Examples

# use some parameters stricter than default:
cpdb_signaling_network <- nichenet_signaling_network_cpdb(
    complex_max_size = 2,
    min_score = .99
)

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