Introduction
2025 was a very busy year for the Submissions Working Group and we have big plans for 2026.
For 2025 recap we have two Pilots nearing completion:
For 2026 we have launched two new Pilots:
- Pilot 6 - expansion of ADaM and Display programs
- Pilot 7 - creation of new simulated data
Read on if you want to learn more about what we submitted to the FDA for 2025 and what we plan on working on for 2026 as well as a few more related bits of news.
Previous Pilots (1 - 3) to the FDA
In case this is your first time hearing about these R-based Submissions to the FDA (Pilots), then we got a quick recap for you! Each Pilot has served to explore how a sponsor can submit an R-based submission package to the FDA via the eCTD portal. The Pilots are small sets of R programs using the original CDISC Pilot data.
Previous successful Pilots to the FDA:
- Pilot 1 delivered Tables and Figures to the FDA using R.
- Pilot 2 delivered the same Tables and Figures using a Shiny App created in R.
- Pilot 3 delivered the Tables and Figures using R as well as the ADaMs…you guessed it using R. .
For information on these Pilots navigate to our Pilot’s background page on submission working group
Pilot 4 (Webassembly and containers)
The R Consortium Submissions Working Group’s Pilot 4 project aims to evaluate the use of both WebAssembly and container technologies to bundle R-language based Shiny applications for submission to the FDA, focusing on enhancing reproducibility and ease of review. The container and WebAssembly portions have been submitted to FDA, with the formal report summarizing findings and conclusions is nearing completion.
Webassembly
Submission and Interactions: The WebAssembly component of Pilot 4 was successfully submitted to the FDA’s Electronic Common Technical Document (eCTD) gateway on September 20, 2024. This marked a significant milestone as it was the first publicly available submission package to include a WebAssembly component, officially received by the FDA Center for Drug Evaluation and Research (CDER) staff.
Findings and Advantages: WebAssembly technology compiles applications into a portable and consistent environment that can be run directly within a web browser, eliminating the need for complex setups on the reviewer’s side. According to Eric Nantz of Eli Lilly and Pilot 4 Lead, using WebAssembly reduces the amount of dependencies required to run a Shiny application in the traditional method (such as the application submitted in Pilot 2), however certain libraries are still required to compile the WebAssembly application and launch a web server process to view the application.
FDA Preference: Surprisingly, FDA reviewers initially found WebAssembly easier to work with compared to container technology. This was contrary to the R Consortium team’s initial expectation, as WebAssembly is a newer framework. Reviewers found WebAssembly more accessible because it only required a web browser, which was readily available to them.
containers
Submission and Interactions: The container technology component represents the second part of the Pilot 4 project. The submission has been sent via the eCTD portal in Summer of 2025, but there is still ongoing discussion for the viability of container technology being used behind the FDA firewall. We plan on releasing a more thorough post on our finding and interactions with the FDA in the coming months.
Findings and Advantages: The objective for containers (such as Docker or Podman) is to package the entire application environment, including system and R-specific dependencies, to ensure consistent and reproducible execution across different systems. Key challenges discovered during the review process for installing dependencies required to run Docker containers in a Windows environment have presented challenges along with fruitful discussion.
FDA Interactions and Preference: The R Consortium team initially anticipated that container technology would be easier for the FDA to administer and install. However, the initial feedback from FDA reviewers indicated a preference for the WebAssembly approach. This suggests that while containers offer robust reproducibility, their setup or execution might present an initial learning curve or more steps for FDA reviewers compared to the browser-based WebAssembly option. Additional FDA feedback on the container component is expected after its submission.
Pilot 5
Pilot 5 is ambitious in it plans to replace all xpts with datasetjson. The pilot started in early 2025 and we were able to submit in the Fall of 2025. The ADaM programs for Pilot 5 write out datasetjson in lieu of xpts for submission to the FDA and we also converted all the SDTM xpts to datasetjson. The SDTM programs are not available for this pilot and so we just did a straigtt conversion of the data using Converting from XPT from the datasetjson R package.
FDA Interactions and Preference: The FDA requested some minor rework with how we use intermediate datasets in the programs, which led to a re-submission in early January 2026. We hope to have completed this submission some time in the Spring of 2026.
Findings and Advantages: There are a few minor findings from conversion of data to datasetjson, which we have documented in the ADRG. We also discovered that the datasetjson v1.1 was not available in the Pinnacle 21 validation software. We discussed this with the FDA and validated with xpts, which you can also find int he ADRG. datasetjson replacing xpts for submission would be a huge win for modernizing workflows and stacks for doing submissions!
Pilot 6
Each Pilot to the FDA has been focused on the delivery of the R-based content so Pilots have been small in nature. For example Pilot 1 only had 4 R programs!
Pilot 6 seeks to expand the number of R programs available for ADaMs and Displays. We just kicked off this Pilot in January of 2026 so if are looking to write R programs for ADaM and Displays in a low-stress environment then come join us! FYI - Pilot 6 is will not be submitted to the FDA, but is laying the groundwork for future pilots if more programs are needed. We also hope to leverage AI and other automation tools to help build a more robust pipeline in preparation for future submissions.
Pilot 7
The R Submissions Working Group Pilot 7, kicked off in January 2026, is focused on closing a key gap in the open-source clinical trial ecosystem: objective, realistic benchmarking data for demonstrating and evaluating modern R-based and AI-enabled workflows across clinical development, analysis, and regulatory submissions.
As adoption of open-source tooling accelerates, demonstration and evaluation are increasingly constrained by the lack of high-quality, publicly available clinical trial datasets. While existing public references (e.g., CDISC Pilot 1) have been valuable, they are often outdated relative to current CDISC standards and industry practice, limited in scale and complexity, and not well-suited for testing today’s end-to-end automation and AI-assisted workflows.
Pilot 7 aims to address this by leveraging statistical simulation methods together with advanced AI capabilities to generate “realistic-looking” datasets that align with recent CDISC standards. These benchmark datasets will support future pilots within the R submissions Working Group, and are also intended to be broadly useful for tool demonstrations, method evaluation, and education across the clinical trial community.
Please take our survey so we can better understand and create data needed to meet today’s modern pipelines.Link to Survey
Other great achievements
R packages submitted through ectd portal
A milestone! FDA expands accepted R file formats, resulting directly from joint work between industry and FDA through the R Consortium Submissions Working Group. Submitting an R package via the eCTD portal just got a little easier - Expanded FDA eCTD File Format Support for R Packages — A Milestone Achieved Through Industry–FDA Collaboration
Hex Stickers
Huge shout out to J&J to help us create some really beautiful hex stickers. Feels like a legitimate project when you got some hexes!
How to Join!
Join the R Submissions Working Group
The R Submissions Working Group comprises members from over 10 pharmaceutical companies, as well as regulatory agencies. We are a collaborative community open to anyone interested in contributing to this important work. For more information, or to get involved, visit our website or contact us directly at director@r-consortium.org.
More about the R Submissions Working Group
The R Consortium R Submissions Working Group is focused on improving practices for R-based clinical trial regulatory submissions.
Health authority agencies from different countries require electronic submission of data, computer programs, and relevant documentation to bring an experimental clinical product to market. In the past, submissions have mainly been based on the SAS language.
In recent years, the use of open source languages, especially the R language, has become very popular in the pharmaceutical industry and research institutions. Although the health authorities accept submissions based on open source programming languages, sponsors may be hesitant to conduct submissions using open source languages due to a lack of working examples.
Therefore, the R Submissions Working Group aims to provide R-based submission examples and identify potential gaps while submitting these example packages. All materials, including submission examples and communications, are publicly available on the R consortium GitHub page.