Comprehensive documentation of R/Pharma 2025 conference workshops, presentations, and insights.

📍 View the full site: actn3bioinformatics.github.io/R-Pharma-2025-Workshops

• 19 Hands-on Workshops
• 8 Europe/US Thematic Sessions
• 30+ Presentations
• November 2025 Conference Date

• 🤖 AI & LLM Integration - 8+ sessions on artificial intelligence in pharma R workflows
• 📊 Clinical Reporting - Modern approaches to TLGs, CSRs, and regulatory submissions
• ✅ Validation & Compliance - GxP-ready R solutions and regulatory acceptance
• 🚀 Open Source Adoption - Industry shift from proprietary to open-source tools

Detailed documentation of 19 workshops covering:

• AI & LLM - Getting started with {ellmer}, building agentic systems, privacy-preserving implementations
• Clinical Reporting - {officer}, {flextable}, {cardinal}, {gtsummary}, Quarto
• Development & Validation - Package building, validation frameworks, {datasetjson}
• Statistical Methods - Stan debugging, Bayesian approaches, {rpact}, {tidymodels}
• Specialized Apps - {teal}, SDTM programming, Python for CSR, HPC integration

Summaries from:

• 8 Europe/US thematic sessions
• 13 Asia/Pacific presentations
• Topics from AI agents to GSK's open-source journey

• Trend Analysis - AI revolution, open-source momentum, regulatory evolution
• Tools Catalog - A-Z reference of all mentioned packages and technologies
• Career Guidance - Skills demand, transition strategies, contribution opportunities

Visit: actn3bioinformatics.github.io/R-Pharma-2025-Workshops

# Clone the repository
git clone https://github.com/ACTN3Bioinformatics/R-Pharma-2025-Workshops.git
cd R-Pharma-2025-Workshops

# Install Quarto (if not already installed)
# Download from: https://quarto.org/docs/get-started/

# Render the site
quarto render

# Preview locally
quarto preview

The site will be available at http://localhost:4200

.
├── _quarto.yml              # Quarto configuration
├── index.qmd                # Home page
├── styles.css               # Custom styling
├── workshops/               # Workshop documentation
│   ├── ai-llm/
│   ├── clinical-reporting/
│   ├── development-validation/
│   ├── statistical-methods/
│   └── specialized/
├── presentations/           # Presentation summaries
│   ├── europe-us-sessions.qmd
│   └── asia-pacific-sessions.qmd
├── summary/                 # Analysis and insights
│   ├── trends-insights.qmd
│   ├── tools-catalog.qmd
│   └── career-insights.qmd
└── about.qmd               # About this project

• Getting Started with LLM APIs in R - Beginner-friendly intro to {ellmer}
• Advanced Clinical Reporting with officer & flextable - Professional Word reports
• Introduction to Building R Packages - Create your first package
• From Data to Insights with {teal} - Interactive clinical trial apps

• GSK's Journey to Open Source - 50%+ R code adoption story
• GenAI in Production - Moving beyond prototypes in pharma
• Mosaic: ARS-Driven TFL Automation - CDISC standards implementation
• LLM-Powered {gtsummary} - QC-ready tables in minutes

• {ellmer} - LLM integration for R
• {cards} - Analysis Results Data
• {crane} - Extension to {gtsummary}
• {polars} - High-performance data frames
• {mcpr} - Model Context Protocol in R

• Quarto - Publishing system
• GitHub Pages - Hosting
• GitHub Actions - Automated deployment
• Custom CSS - R blue accent color (#276DC2)

This repository was created to document and share knowledge from the R/Pharma 2025 conference. It serves as a comprehensive resource for:

• 🎓 Conference attendees reviewing materials
• 🔍 Researchers exploring R solutions for pharma
• 💼 Hiring managers assessing industry trends
• 🚀 Developers discovering tools and best practices

Szymon Myrta

• 8+ years of experience in bioinformatics in pharmaceutical and biotech settings
• NGS data analysis (RNAseq, scRNA-seq, ChIP-seq, TCR/BCR-seq, WES/WGS etc.) [Bioconductor, Seurat, edgeR, DESeq2, limma]
• Functional genomics data analysis (CRISPR / ORF overexpression screens)
• Strong R programming skills, including development of R packages and Shiny apps
• Developer of NGS data analysis pipelines and reproducible research workflows and documentation (RMarkdown, Quarto, Snakemake, Bash, Git, CI/CD, Docker)
• Data visualization and interpretation of results [ggplot2, Shiny, ComplexHeatmap]
• Background in computational biology, cancer genomics, immuno-oncology
• Co-author of multiple peer-reviewed scientific publications in top-tier journals
• [Interested in multi-omics data integration, precision medicine, AI-powered analyses]{.underline}

Found an error or have suggestions? Contributions are welcome!

1. Fork the repository
2. Create a feature branch (git checkout -b feature/improvement)
3. Commit your changes (git commit -m 'Add improvement')
4. Push to the branch (git push origin feature/improvement)
5. Open a Pull Request

This project is licensed under the MIT License - see the LICENSE file for details.

• R/Pharma 2025 conference organizers and speakers
• All workshop instructors who shared their expertise
• The open-source R community
• Pharmaverse initiative

For questions or feedback: - Open an issue - Connect on LinkedIn

⭐ If you find this repository useful, please consider giving it a star!

Last updated: November 2025