**7. Drug repositioning examples with reproducible code**

Due to the pandemic of COVID-19 and no effective drugs for this disease, drug repositioning is a great way to combat this disease. Several researchers have used cogena for drug repositioning to fight the COVID-19 [56, 74].

We used the metatranscriptome data of the bronchoalveolar lavage fluid from 8 severe COVID-19 patients and 20 healthy controls to obtain the gene expression signature of COVID-19 [75]. The co-expression analysis, pathway analysis and drug repositioning analysis were done using the cogena pipeline [56]. We identified several drugs which were associated with COVID-19 reported before. For example, Saquinavir, a protease inhibitor, is a drug for human immunodeficiency virus infection. This drug was also identified by several docking methods [76]. Dexamethasone is a "major development" in the fight against COVID-19 in the RECOVERY trial [77]. Ribavirin can be used to treat SARS-CoV and MERS-CoV infections [78]. Importantly, it is a recommended drug in the diagnosis and treatment protocol for COVID pneumonia (trial version 5–latest) published by the National Health Commission of the P.R. of China. It was also identified by several docking methods [79]. Furthermore, we identified several other candidate drugs for COVID-19, for example, dinoprost, a smooth muscle activator, and (−)-isoprenaline, a bronchodilator for obstructive lung diseases. These candidate drugs could be tested in vitro and in vivo to validate their possibility.

The whole pipeline of this gene-signature-based drug repositioning for COVID-19 using cogena is accessible at https://github.com/zhilongjia/COVID-19 with data and code, forming a good resource for drug repositioning and reproducible study.

There are also other examples of drug repositioning using cogena with reproducible codes. For instance, the code of the drug repositioning for psoriasis is

### *Gene Signature-Based Drug Repositioning DOI: http://dx.doi.org/10.5772/intechopen.101377*

available at https://github.com/zhilongjia/psoriasis and the code of drug repositioning for periodontitis is available at https://github.com/zhilongjia/Fn\_HGFcell. These examples will enhance our understanding of how drug repositioning works and how to implement drug repositioning.
