NeDRex

Finds drug repurposing candidates and disease modules. Builds custom heterogeneous molecular networks
NeDRex is the first generically applicable integrated platform for network-based disease module discovery and drug repurposing. It is build of three main components: a knowledgebase ([https://nedrex.net/tutorial/intro.html#nedrexdb NeDRexDB]), a Cytoscape app ([https://nedrex.net/tutorial/ NeDRexApp]), and an API ([https://api.nedrex.net/ NeDRexAPI]). NeDRexApp provides implementations of diverse network algorithms, such as Multi-Steiner Trees ([https://www.nature.com/articles/s41467-020-17189-2 MuST]), [https://www.nature.com/articles/s41467-020-17189-2 TrustRank], Biclustering Constrained by Networks ([https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa1076/6050718 BiCoN]), and Disease Module Detection ([https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004120 DIAMOnD]). All algorithms except for BiCoN (uses gene expression data) require a list of user-selected genes (referred to as seeds) as starting point. Seeds can be all or a subset of the genes associated with the disease, so-called disease genes, or genes contained in disease modules. Moreover, NeDRex allows researchers to leverage their *expert knowledge* for discovering drug repurposing candidates via network medicine methods. Our platform can also be used to identify disease modules and possibly repurposable drugs for any newly discovered disease such as COVID-19. Finally, to validate the statistical significance of the lists of drugs and disease modules returned by NeDRex, three validation methods are implemented. These validation methods allow users to judge quantitatively the performance of the algorithms they employed for their individual use cases.

1.1.1

Works with Cytoscape 3.6

Release Notes

Updates to the statistical validation methods

1.1.0

Works with Cytoscape 3.6

Release Notes

Added different statistical validation methods for the evaluation of drug repurposing results.

1.0.0

Works with Cytoscape 3.6


CYTOSCAPE 3

Version 1.1.1

License Click here

Released 1 Oct 2021

Works with Cytoscape 3.6

Download Stats Click here