ndexr

ndexr provides programmatic access to the NDEx biological network repository and enables retrieval, conversion to igraph, modification, and upload of networks for computational analysis.

Key Features:

• Network Integration: Integrates biological networks as prior-knowledge inputs into bioinformatic analyses and preserves network outputs produced by analyses.
• Network Retrieval and Conversion: Searches the NDEx repository and retrieves networks in formats compatible with the igraph R package for downstream network analysis.
• Modification and Upload Capabilities: Allows modification and extension of retrieved networks within R and uploads modified networks back to NDEx servers.

Scientific Applications:

• Systems Biology: Incorporates curated interaction networks from NDEx into systems-level modeling and network-based analyses.
• Genomics: Maps genomic data onto network topologies retrieved from NDEx to support network-guided interpretation of genomic results.
• Personalized Medicine: Enables integration of patient-specific data with NDEx networks to support network-informed precision analyses.

Methodology:

Interfaces with NDEx servers via an R package providing functions to search NDEx, retrieve networks in igraph-compatible formats, modify or extend networks in R, and upload modified networks back to NDEx.