Tools & Packages Catalog

Complete A-Z reference of tools mentioned at R/Pharma 2025

Overview

This catalog documents all R packages, Python libraries, and tools mentioned across the 19 workshops and 30+ presentations at R/Pharma 2025. Entries include descriptions, primary use cases, and links to where they were discussed.

NotePopularity Indicators

Packages are marked with mentions:

  • πŸ”₯πŸ”₯πŸ”₯ 5+ mentions
  • Hot topic, widespread interest
  • πŸ”₯πŸ”₯ 3-4 mentions
  • Multiple sessions
  • πŸ”₯ 1-2 mentions
  • Emerging or specialized

R Packages

A

{admiral} πŸ”₯πŸ”₯

ADaM in R Asset Library

Modular R package for creating ADaM datasets. Part of pharmaverse ecosystem, transitioning from active development to stable maintenance.

B

{beeca} πŸ”₯

Bayesian Covariate Adjustment

Lightweight R package implementing FDA 2023 covariate adjustment guidance.

{bmstate} πŸ”₯

Bayesian Multistate Models

Stan-based package for Bayesian survival and multistate models in clinical trials.

C

{cardinal} πŸ”₯πŸ”₯

Standardized Clinical TLG Templates

Open-source collection of table, listing, and graph templates aligned with CDISC standards.

{cards} πŸ”₯πŸ”₯πŸ”₯

Analysis Results Data Objects

Creates language-agnostic Analysis Results Data (ARD) objects for clinical reporting.

  • Use Cases: ARD generation, QC, multi-language results
  • Mentioned in: Cardinal workshop, {crane}, PMDA inquiries, LLM-powered tables
  • Links: Part of {gtsummary} ecosystem

{cgmguru} πŸ”₯

Continuous Glucose Monitoring Analysis

Automated glycemic event detection from CGM data.

{chromote} πŸ”₯

Chrome Remote Interface

Headless Chrome control for testing Shiny apps.

{crane} πŸ”₯πŸ”₯

Extension to {gtsummary}

Pharmaceutical-specific extensions to {gtsummary} with ARD-based QC.

D

{datasetjson} πŸ”₯

CDISC Dataset-JSON Support

Read and write CDISC Dataset-JSON format in R and Python.

{devtools} πŸ”₯πŸ”₯

Package Development Tools

Essential package for R package development.

{dplyr} πŸ”₯πŸ”₯

Data Manipulation

Core tidyverse package for data transformation.

  • Use Cases: Data wrangling, pipelines
  • Mentioned in: Multiple workshops (implicit in many examples)

{duckplyr} πŸ”₯

DuckDB with dplyr Syntax

dplyr backend using DuckDB for performance.

E

{ellmer} πŸ”₯πŸ”₯πŸ”₯πŸ”₯πŸ”₯

LLM Integration for R

Unified interface for working with Large Language Models from R.

F

{flextable} πŸ”₯πŸ”₯πŸ”₯

Flexible Tables

Create publication-quality tables with fine-grained control.

G

{ggplot2} πŸ”₯πŸ”₯

Grammar of Graphics

The standard for data visualization in R.

  • Use Cases: Publication-ready plots, clinical graphics
  • Mentioned in: officer/flextable workshop, multiple examples

{gt} πŸ”₯

Grammar of Tables

Modern table creation with flexible styling.

  • Use Cases: HTML tables, dashboards
  • Mentioned in: Cardinal workshop (gt backend for gtsummary)
  • Links: gt.rstudio.com

{gtsummary} πŸ”₯πŸ”₯πŸ”₯πŸ”₯

Summary Tables

Create publication-ready summary tables with minimal code.

L

{llumen} πŸ”₯πŸ”₯

Agentic LLM Framework (Internal)

Merck KGaA’s internal package for biomedical documents, databases, and foundation models.

  • Use Cases: Document extraction, database querying, RAG, histopathology
  • Mentioned in: Presentations - llumen
  • Status: Internal Merck package

M

{mcpr} πŸ”₯πŸ”₯

Model Context Protocol in R

R implementation of Model Context Protocol for AI integration.

{meRlin} πŸ”₯

AI Assistant for Clinical Programming

Context-aware AI assistant specifically for clinical programming.

O

{officer} πŸ”₯πŸ”₯πŸ”₯

Manipulate Microsoft Word Documents

Create and modify Word documents programmatically.

P

{parsnip} πŸ”₯

Unified ML Interface

Part of tidymodels, provides consistent interface for models.

{pkgdown} πŸ”₯

Package Websites

Generate websites from R package documentation.

{PKNCA} πŸ”₯

Pharmacokinetic Non-Compartmental Analysis

Calculate 200+ PK parameters for NCA.

{pointblank} πŸ”₯πŸ”₯

Data Validation and Documentation

Comprehensive data quality and documentation workflows.

R

{ragnar} πŸ”₯πŸ”₯

Retrieval-Augmented Generation

Vector database and RAG functionality for R.

{recipes} πŸ”₯

Preprocessing for Modeling

Part of tidymodels, feature engineering and preprocessing.

{riskassessment} πŸ”₯πŸ”₯

Package Risk Assessment

Shiny app for package validation and risk assessment.

  • Use Cases: Validation workflows, package quality assessment
  • Mentioned in: Workshop - R Validation
  • Links: R Validation Hub

{riskmetric} πŸ”₯πŸ”₯

Risk Metrics for Packages

Calculate risk metrics for R package validation.

{RobinCar2} πŸ”₯

Covariate Adjustment Methods

ASA-BIOP working group package for covariate adjustment.

{roxygen2} πŸ”₯πŸ”₯

Documentation Generation

Generate R documentation from code comments.

{rpact} πŸ”₯

Clinical Trial Design and Simulation

Comprehensive package for adaptive and group sequential designs.

{rsample} πŸ”₯

Data Splitting and Resampling

Part of tidymodels, train/test splitting and cross-validation.

S

{sdtm.oak} πŸ”₯

SDTM Programming Framework

EDC-agnostic SDTM dataset creation with reusable algorithms.

  • Use Cases: SDTM programming, CDISC compliance
  • Mentioned in: Workshop - SDTM oak
  • Links: Pharmaverse

{shiny} πŸ”₯πŸ”₯πŸ”₯

Interactive Web Applications

Framework for building interactive web apps in R.

  • Use Cases: Dashboards, clinical data exploration, interactive tools
  • Mentioned in: Multiple workshops (teal, HPC, DataChat, validating Shiny)

{shinychat} πŸ”₯πŸ”₯πŸ”₯

Chatbot Interface for Shiny

Add conversational interfaces to Shiny apps.

  • Use Cases: LLM interfaces, chatbots, conversational UIs
  • Mentioned in: Workshop - LLM APIs, DataChat
  • Developer: Posit

{synthpop} πŸ”₯

Synthetic Data Generation

Generate synthetic datasets using machine learning.

T

{teal} πŸ”₯πŸ”₯

Interactive Clinical Trial Apps

Framework for building interactive data exploration apps.

  • Use Cases: Clinical data exploration, interactive analysis
  • Mentioned in: Workshop - teal
  • Version: 1.0 released
  • Developer: Roche/Genentech
  • Links: Part of pharmaverse

{testthat} πŸ”₯πŸ”₯

Unit Testing

Standard testing framework for R packages.

{tidymodels} πŸ”₯πŸ”₯

Machine Learning Framework

Comprehensive ecosystem for modeling and ML in R.

U

{usethis} πŸ”₯πŸ”₯

Package Development Workflow

Automate package setup and development tasks.

V

{val.criterion} πŸ”₯

Validation Criteria

Define validation criteria for package assessment.

  • Use Cases: Validation standards, quality thresholds
  • Mentioned in: Workshop - R Validation
  • Links: R Validation Hub

{val.meter} πŸ”₯

Validation Metrics

Store and retrieve validation metrics.

  • Use Cases: Metric repository, shared validation database
  • Mentioned in: Workshop - R Validation
  • Links: R Validation Hub

Y

{yardstick} πŸ”₯

Model Performance Metrics

Part of tidymodels, calculate model performance metrics.

Python Libraries

polars πŸ”₯πŸ”₯

High-Performance DataFrames

Blazingly fast DataFrame library with Apache Arrow backend.

plotnine πŸ”₯

Grammar of Graphics for Python

ggplot2 equivalent for Python.

Great Tables πŸ”₯πŸ”₯

Modern Table Creation

Python package for creating publication-ready tables.

  • Use Cases: TFLs, clinical reporting
  • Mentioned in: Workshop - Polars
  • Developer: Posit
  • Links: Launched at conference

rtflite πŸ”₯

RTF Generation

Python library for RTF document generation.

LangChain πŸ”₯

LLM Application Framework

Popular Python framework for building LLM applications.

LangGraph πŸ”₯

Multi-Agent Orchestration

Framework for building multi-agent LLM systems.

uv πŸ”₯

Python Package Manager

Fast Python package and project manager.

External Tools & Platforms

Quarto πŸ”₯πŸ”₯πŸ”₯πŸ”₯

Publishing System

Modern scientific publishing system supporting multiple formats.

Stan πŸ”₯πŸ”₯

Bayesian Inference

Platform for statistical modeling and Bayesian inference.

AWS Bedrock πŸ”₯πŸ”₯

Managed LLM Service

Amazon’s managed service for foundational models.

Docker πŸ”₯πŸ”₯

Containerization

Platform for deploying applications in containers.

GitHub Actions πŸ”₯πŸ”₯

CI/CD

Automation platform for building, testing, and deploying.

  • Use Cases: Automated testing, validation, deployment
  • Mentioned in: Multiple workshops (package dev, validation)

Posit Workbench πŸ”₯πŸ”₯

Development Platform

Commercial RStudio IDE for teams (formerly RStudio Workbench).

  • Use Cases: Team collaboration, enterprise R/Python development
  • Mentioned in: GSK journey, multiple enterprise examples
  • Links: posit.co

Posit Connect πŸ”₯

Publishing Platform

Share R/Python content (Shiny, reports, APIs).

  • Use Cases: Shiny deployment, report distribution
  • Mentioned in: HPC workshop, enterprise deployments

RPACT Cloud πŸ”₯

Trial Design Platform

User-friendly platform for {rpact} trial design.

MCP (Model Context Protocol) πŸ”₯πŸ”₯

AI Integration Standard

Standardized protocol for AI tool integration.

  • Use Cases: Cross-platform AI tools, standardized interfaces
  • Mentioned in: Multiple AI/LLM workshops and presentations
  • Links: modelcontextprotocol.io

Claude Code πŸ”₯

AI Coding Assistant

Anthropic’s coding assistant using Claude.

  • Use Cases: AI-assisted coding, MCP integration
  • Mentioned in: MCP presentations

Cursor πŸ”₯

AI Code Editor

AI-powered code editor with MCP support.

  • Use Cases: AI-assisted development
  • Mentioned in: MCP presentations, Roche AI assistant

Specialized Applications

aNCA πŸ”₯

Non-Compartmental Analysis App

Open-source Shiny app for PK analysis.

autoslideR πŸ”₯πŸ”₯

Slide Deck Automation

R package for automating clinical reporting slide decks.

DataChat πŸ”₯

Conversational Clinical Data Interface

Shiny app for natural language queries on clinical data.

Databot πŸ”₯

Data Analysis Assistant

Posit’s LLM-powered data analysis tool.

Mosaic πŸ”₯

ARS-Driven TFL Platform

Novartis platform for automated TFL generation.

Litmusverse πŸ”₯

Shiny Validation Suite

Jumping Rivers’ suite for Shiny app validation.

Standards & Specifications

CDISC ARS/ARM πŸ”₯πŸ”₯πŸ”₯

Analysis Results Standard

Emerging standard for machine-readable analysis results.

  • Impact: Driving automation (Mosaic, {cards}, {crane})
  • Mentioned in: Multiple workshops and presentations

CDISC SDTM πŸ”₯πŸ”₯

Study Data Tabulation Model

Standard for clinical trial data submission.

  • Mentioned in: Multiple workshops ({sdtm.oak}, validation, data handling)

CDISC ADaM πŸ”₯πŸ”₯

Analysis Data Model

Standard for analysis datasets.

  • Mentioned in: {admiral}, multiple analysis workshops

πŸ“Š Most Mentioned Tools

Top 10 by Mentions

  1. {ellmer} - 5+ mentions (AI/LLM integration)
  2. Quarto - 4+ mentions (Publishing)
  3. {gtsummary} - 4+ mentions (Clinical tables)
  4. {cards} - 3+ mentions (ARD)
  5. {officer}/{flextable} - 3+ mentions (Word reports)
  6. {shinychat} - 3+ mentions (Chatbots)
  7. {teal} - 2+ mentions (Interactive apps)
  8. Stan - 2+ mentions (Bayesian)
  9. {tidymodels} - 2+ mentions (ML)
  10. {pointblank} - 2+ mentions (Validation)

🎯 By Use Case

AI/LLM Integration

{ellmer}, {mcpr}, {shinychat}, {ragnar}, {llumen}, LangChain, LangGraph, AWS Bedrock, MCP

Clinical Reporting

{gtsummary}, {crane}, {cardinal}, {cards}, {officer}, {flextable}, Quarto, Great Tables, autoslideR

Data Validation

{pointblank}, {riskmetric}, {riskassessment}, Litmusverse

Package Development

{devtools}, {usethis}, {testthat}, {roxygen2}, {pkgdown}

Statistical Analysis

Stan, {rpact}, {tidymodels}, {bmstate}, BayesERtools

CDISC Compliance

{admiral}, {sdtm.oak}, {datasetjson}, ARS/ARM

High Performance

polars, {duckplyr}, Apache Arrow, HPC integration

TipFinding the Right Tool

Use this catalog to:

  • Discover tools for your specific use case
  • Compare alternatives (e.g., {officer} vs Quarto for reports)
  • Identify dependencies (e.g., {gtsummary} uses {cards})
  • Plan your learning path (prerequisites and related tools)

Compiled from R/Pharma 2025 Conference materials | Last updated: November 2025