Streamlining Clinical Trial Data from Raw to Regulatory Submission with R Shiny and Pharmaverse

Streamlining Clinical Trial Data from Raw to Regulatory Submission with R Shiny and Pharmaverse

Arvind Uttiramerur

Programmer Analyst at Thermofisher Scientific, USA

Abstract

In recent years, the pharmaceutical and biotech industries have increasingly adopted open-source tools to enhance the efficiency, transparency, and reproducibility of clinical trial data analysis. R Shiny, a web application framework for R, has become a key component in creating interactive dashboards and visualizations that support real-time data exploration and decision-making. As part of the Pharmaverse ecosystem, R Shiny plays a vital role in regulatory submissions, data analysis, and reporting, offering dynamic, user-friendly interfaces for clinical trial monitoring, patient safety reporting, and efficacy analysis.

This abstract explores the application of R Shiny within the Pharmaverse, emphasizing its seamless integration with tools such as Tplyr and admiral for generating CDISC-compliant SDTM and ADaM datasets. Metadata management and validation are facilitated through OAK, ensuring consistency and traceability. The automated creation of Define.xml using tools like defineR further enhances transparency and regulatory compliance.

Through case studies and practical examples, this abstract highlights how R Shiny and related tools improve data transparency, accelerate decision-making, and support regulatory compliance in clinical trials. By leveraging these open-source technologies, clinical trial teams can streamline data workflows, enhance collaboration, and improve outcomes, ultimately driving innovation within the pharmaceutical industry. The integration of these tools into a cohesive framework significantly enhances the submission process to regulatory bodies like the FDA and EMA, ensuring that clinical data meets both industry and regulatory standards

Conclusion:  

The integration of open-source tools and structured workflows has revolutionized the management, analysis, and reporting of clinical trial data. Metadata management ensures datasets are consistently defined and compliant with regulatory requirements, with tools like OAK offering robust metadata handling and validation that seamlessly integrate into clinical workflows.

Admiral, as part of the Pharmaverse, automates the creation of CDISC-compliant SDTM and ADaM datasets, reducing manual effort and enhancing consistency across clinical trials. The generation of Define.xml files using tools like defineR provides essential documentation of dataset structures, variables, and derivations, improving transparency and traceability for regulatory submissions.

Tables, Listings, and Graphs (TLGs) in formats such as RTF and PDF are efficiently created using tools like Tplyr, ensuring outputs meet both clinical and regulatory standards. Coupled with standardized datasets and metadata, these outputs form a comprehensive submission package for regulatory bodies, simplifying the submission process.

Shiny applications, such as TidyCDISC, further enhance real-time data exploration and visualization, empowering stakeholders to interactively review clinical data, monitor safety signals, and dynamically generate reports.

Together, this ecosystem—from metadata to dataset creation, reporting, and visualization—provides a transparent, efficient, and compliant approach to clinical trial data management. By leveraging these open-source tools, pharmaceutical companies can streamline workflows, reduce costs, ensure regulatory compliance, and maintain the integrity and reproducibility of their data.

Reference

1.       https://www.rstudio.com/assets/img/validation-shiny-rmd.pdf

2.       https://cosa.cdisc.org/directory/admiral

3.       https://www.rstudio.com/assets/img/validation-tidy.pdf

4.       https://www.r-project.org/doc/R-FDA.pdf