Skill: jackkuo666/rstudio-research-agent (version 0.1.0)

--- name: rstudio-research-agent description: Interact with R and RStudio environments for scientific research tasks including creating projects, running analyses, managing dependencies, and generating publication-quality plots. --- # RStudio Research Agent A Claude Code skill for comprehensive R-based research workflow automation. This skill enables interaction with R and RStudio environments for scientific computing, statistical analysis, bioinformatics, and data visualization. ## Overview This skill helps researchers and data scientists: - Create structured, reproducible R research projects - Execute R scripts and RMarkdown analyses - Debug environment and dependency issues - Generate publication-quality plots and reports - Manage R packages with renv for reproducibility Use this skill when the user wants to: - Create a new R project with standard structure - Run R analyses on existing projects - Troubleshoot R package dependencies - Generate statistical reports or visualizations - Set up reproducible R workflows --- ## What This Skill Does When activated, this skill provides four main capabilities: ### 1. Create R Research Projects - Scaffold new R projects with standard folder structure - Initialize Git repositories (optional) - Set up `renv` for package management - Generate template scripts and reports - Create `.Rproj` files for RStudio ### 2. Run Analyses in Existing Projects - Execute R scripts and RMarkdown files - Handle parameterized analyses - Return results, tables, and plots - Generate HTML/PDF reports ### 3. Debug Environment and Dependencies - Check for missing R packages - Resolve library conflicts - Suggest fixes for environment issues - Verify R version compatibility ### 4. Generate Publication-Quality Plots - Create figures with ggplot2 and other visualization libraries - Export to PDF/PNG/SVG/TIFF formats - Follow journal-specific formatting guidelines - Support multi-panel composite figures - Use color-blind friendly palettes --- ## Example User Requests That Should Trigger This Skill - "Create a new R project for my genomics data analysis" - "Run `analysis.R` in my existing project and show results" - "Check if all required packages are installed" - "Generate a scatter plot with regression line from my dataset" - "Set up a reproducible R workflow for RNA-seq analysis" - "Debug my R environment - packages won't load" - "Create a statistical report for this clinical trial data" --- ## Project Structure Projects created by this skill follow this standardized structure: ``` my-research-project/ ├── data/ │ ├── raw/ # Original, immutable data files │ └── processed/ # Cleaned, transformed data ├── scripts/ # Analysis and processing scripts ├── results/ │ ├── figures/ # Plots and visualizations │ ├── tables/ # Summary tables │ └── models/ # Saved model objects (.rds files) ├── reports/ # R Markdown/Quarto documents ├── renv.lock # Package version lock file ├── .Rproj # RStudio project file └── README.md # Project documentation ``` --- ## Tools & Packages Commonly Used | Purpose | R Packages | |--------|------------| | Data wrangling | tidyverse, data.table | | Visualization | ggplot2, patchwork, scales | | Statistics | stats, lme4, survival, broom | | Bioinformatics | Bioconductor (DESeq2, edgeR, limma) | | Reporting | rmarkdown, quarto | | Reproducibility | renv | --- ## Example Workflows ### Creating a New Project **User:** Create a new R project for gene expression analysis with Git initialized. **Skill actions:** 1. Create directory structure (data/, scripts/, results/, reports/) 2. Initialize Git repository 3. Set up renv environment 4. Install DESeq2, tidyverse, ggplot2 5. Generate analysis template scripts 6. Create R Markdown report template ### Running an Analysis **User:** Run the differential expression analysis and return results. **Skill actions:** 1. Activate project environment (renv) 2. Execute analysis script 3. Capture console output and plots 4. Return summary tables and model statistics 5. Generate report if requested ### Debugging Dependencies **User:** My R script fails with "package not found" errors. **Skill actions:** 1. Check R version and package library paths 2. Scan script for required packages 3. Compare with installed packages 4. Generate installation commands 5. Check for version conflicts --- ## Notes - Requires R >= 4.0.0 - Supports both RStudio and command-line R - Uses `renv` for reproducible package management - All outputs saved to files (not just console) - Follows R best practices and modern conventions --- ## Sub-Skills This skill includes specialized sub-skills: - **create-project**: Scaffold new R research projects - **run-analysis**: Execute R scripts and generate reports - **debug-env**: Troubleshoot R environments and dependencies - **generate-plots**: Create publication-quality figures with journal formatting Each sub-skill can be invoked independently or as part of a complete workflow.


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (MEDIUM)