OmnipathR

OmnipathR provides a client for the OmniPath web service and multiple molecular interaction and annotation resources, enabling retrieval, transformation, and analysis of pathway and network data in R.

Key Features:

• OmniPath Web Service Client: Queries and downloads data from the OmniPath web service (https://www.omnipathdb.org).
• Data Transformation Functions: Transforms and pretty prints downloaded data for downstream analysis.
• Multi-Resource Access: Provides functions to access 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.
• NicheNet Integration: Features close integration with the NicheNet method for ligand activity prediction from transcriptomics data and its R implementation nichenetr.

Scientific Applications:

• Pathway and Network Analysis: Supports construction and analysis of molecular interaction networks from curated pathway databases.
• Ligand Activity Prediction: Enables prediction of ligand activities from transcriptomics data through integration with NicheNet.
• Gene Regulatory Network Analysis: Facilitates access to transcription factor-target interactions from resources such as HTRIdb, RegNetwork, TRRUST, and TF census.
• Protein-Protein Interaction Analysis: Retrieves protein interaction data from BioPlex, InWeb InBioMap, and other resources.
• Pharmacological Data Integration: Incorporates drug-target and receptor-ligand information from the Guide to Pharmacology (IUPHAR/BPS).

Methodology:

OmnipathR functions as a client that queries web services and resources, downloads data, and applies transformation and pretty printing functions to the retrieved data.