This skill helps create and manage a complete R-based research analysis workflow. It is designed for scientific computing, statistical modeling, bioinformatics, and data visualization tasks.

Use this skill when the user wants to:

• Analyze datasets using R
• Perform statistical tests or modeling
• Run bioinformatics or omics analysis in R
• Generate plots, figures, or reports
• Create a reproducible R project structure
• Install and manage R package dependencies

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What This Skill Does

When activated, this skill will:

• Create a structured R project

- data/ for raw and processed data - scripts/ for analysis code - results/ for outputs - reports/ for R Markdown or Quarto reports

• Set up environment

- Initialize .Rproj (if using RStudio) - Create renv environment for reproducibility - Install required CRAN/Bioconductor packages

• Generate analysis scripts

- Data loading and cleaning - Statistical analysis or modeling - Visualization with ggplot2 - Save outputs (CSV, plots, model summaries)

• Create a report

- R Markdown / Quarto document - Includes methods, results, and figures - Render to HTML or PDF

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Example User Requests That Should Trigger This Skill

• "Use R to analyze this CSV and generate plots"
• "Run differential expression analysis in R"
• "Create a statistical report for this dataset"
• "Build an R project for microbiome analysis"
• "Fit a regression model in R and summarize results"

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Example Workflow

User: Analyze this gene expression dataset and produce figures.

Skill actions:

• Create project structure
• Install tidyverse, DESeq2, ggplot2
• Write analysis script
• Generate PCA plot and volcano plot
• Produce an HTML report

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Tools & Packages Commonly Used

Purpose	R Packages
Data wrangling	tidyverse, data.table
Visualization	ggplot2, patchwork
Statistics	stats, lme4, survival
Bioinformatics	Bioconductor packages (DESeq2, edgeR, limma)
Reporting	rmarkdown, quarto
Reproducibility	renv

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Notes

• Prefer reproducible workflows (renv, scripted analysis)
• Avoid interactive-only steps unless requested
• All outputs should be saved to files, not just printed to console