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      {
        "title": "Creating R Research Projects",
        "body": "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.\n\nUse this skill when the user wants to:\n\nAnalyze datasets using R\nPerform statistical tests or modeling\nRun bioinformatics or omics analysis in R\nGenerate plots, figures, or reports\nCreate a reproducible R project structure\nInstall and manage R package dependencies"
      },
      {
        "title": "What This Skill Does",
        "body": "When activated, this skill will:\n\nCreate a structured R project\n\ndata/ for raw and processed data\nscripts/ for analysis code\nresults/ for outputs\nreports/ for R Markdown or Quarto reports\n\n\n\nSet up environment\n\nInitialize .Rproj (if using RStudio)\nCreate renv environment for reproducibility\nInstall required CRAN/Bioconductor packages\n\n\n\nGenerate analysis scripts\n\nData loading and cleaning\nStatistical analysis or modeling\nVisualization with ggplot2\nSave outputs (CSV, plots, model summaries)\n\n\n\nCreate a report\n\nR Markdown / Quarto document\nIncludes methods, results, and figures\nRender to HTML or PDF"
      },
      {
        "title": "Example User Requests That Should Trigger This Skill",
        "body": "\"Use R to analyze this CSV and generate plots\"\n\"Run differential expression analysis in R\"\n\"Create a statistical report for this dataset\"\n\"Build an R project for microbiome analysis\"\n\"Fit a regression model in R and summarize results\""
      },
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        "title": "Example Workflow",
        "body": "User: Analyze this gene expression dataset and produce figures.\n\nSkill actions:\n\nCreate project structure\nInstall tidyverse, DESeq2, ggplot2\nWrite analysis script\nGenerate PCA plot and volcano plot\nProduce an HTML report"
      },
      {
        "title": "Tools & Packages Commonly Used",
        "body": "PurposeR PackagesData wranglingtidyverse, data.tableVisualizationggplot2, patchworkStatisticsstats, lme4, survivalBioinformaticsBioconductor packages (DESeq2, edgeR, limma)Reportingrmarkdown, quartoReproducibilityrenv"
      },
      {
        "title": "Notes",
        "body": "Prefer reproducible workflows (renv, scripted analysis)\nAvoid interactive-only steps unless requested\nAll outputs should be saved to files, not just printed to console"
      }
    ],
    "body": "Creating R Research Projects\n\nThis 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.\n\nUse this skill when the user wants to:\n\nAnalyze datasets using R\nPerform statistical tests or modeling\nRun bioinformatics or omics analysis in R\nGenerate plots, figures, or reports\nCreate a reproducible R project structure\nInstall and manage R package dependencies\nWhat This Skill Does\n\nWhen activated, this skill will:\n\nCreate a structured R project\n\ndata/ for raw and processed data\nscripts/ for analysis code\nresults/ for outputs\nreports/ for R Markdown or Quarto reports\n\nSet up environment\n\nInitialize .Rproj (if using RStudio)\nCreate renv environment for reproducibility\nInstall required CRAN/Bioconductor packages\n\nGenerate analysis scripts\n\nData loading and cleaning\nStatistical analysis or modeling\nVisualization with ggplot2\nSave outputs (CSV, plots, model summaries)\n\nCreate a report\n\nR Markdown / Quarto document\nIncludes methods, results, and figures\nRender to HTML or PDF\nExample User Requests That Should Trigger This Skill\n\"Use R to analyze this CSV and generate plots\"\n\"Run differential expression analysis in R\"\n\"Create a statistical report for this dataset\"\n\"Build an R project for microbiome analysis\"\n\"Fit a regression model in R and summarize results\"\nExample Workflow\n\nUser: Analyze this gene expression dataset and produce figures.\n\nSkill actions:\n\nCreate project structure\nInstall tidyverse, DESeq2, ggplot2\nWrite analysis script\nGenerate PCA plot and volcano plot\nProduce an HTML report\nTools & Packages Commonly Used\nPurpose\tR Packages\nData wrangling\ttidyverse, data.table\nVisualization\tggplot2, patchwork\nStatistics\tstats, lme4, survival\nBioinformatics\tBioconductor packages (DESeq2, edgeR, limma)\nReporting\trmarkdown, quarto\nReproducibility\trenv\nNotes\nPrefer reproducible workflows (renv, scripted analysis)\nAvoid interactive-only steps unless requested\nAll outputs should be saved to files, not just printed to console"
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    "version": "0.1.0",
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