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]),
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.
**If you use NeDRex in your research, please cite:**
Sadegh, Sepideh, et al. "Network medicine for disease module identification and drug repurposing with the NeDRex platform." Nature communications 12.1 (2021): 1-12.
Paper URL: [https://www.nature.com/articles/s41467-021-27138-2]