saezlab/OmnipathR: OmniPath web service client and more

A client for the OmniPath web service ( and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).

Getting started

Package details

Bioconductor views Annotation DataImport DataRepresentation GeneRegulation GeneSignaling GraphAndNetwork KEGG Network Pathways SingleCell Software SystemsBiology ThirdPartyClient Transcriptomics
LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
saezlab/OmnipathR documentation built on June 16, 2021, 3:29 a.m.