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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

This is an R package (p3003PBC) containing educational materials for the FGCZ (Functional Genomics Center Zurich) Protein Bioinformatics Course. The package includes lecture slides and R exercises covering experimental design, hypothesis testing, linear models, multiplicity correction, sample size estimation, and GSEA.

Package Structure

  • R/: Core R functions

    • utilities.R: Contains sample_stats() function for statistical simulations
    • BHExtracted.R: Implementation of Benjamini-Hochberg p-value adjustment
    • hello.R: Template function

  • vignettes/: Course lecture materials as R Markdown (xaringan) presentations

    • ExpDesign.Rmd: Experimental design lecture
    • Hypothesis_Testing_p3003.Rmd: Hypothesis testing lecture
    • IntroductionToLinearModels.Rmd: Linear models lecture
    • Multiplicity_p3003.Rmd: Multiple testing correction lecture
    • SampleSizeEstimation.Rmd: Sample size estimation lecture
    • GSEA_with_msig.Rmd: Gene set enrichment analysis lecture
    • OtherSoftware.Rmd: Overview of other proteomics software
    • BriefIntroductionTooR.Rmd: R programming introduction
    • renderAllVignettest.R: Script to render all vignette presentations

  • inst/: Additional resources

    • images/: Lecture slide images
    • fgcz_formatting/: FGCZ branding files (CSS, headers, footers)
    • BaseR_JG/: Base R workshop materials and example data

Common Development Commands

Building and Installing the Package

# Install package with source code
devtools::install()

# Or from command line
R CMD INSTALL --no-multiarch --with-keep.source .

Rendering Lecture Materials

# Render individual vignette
rmarkdown::render("vignettes/ExpDesign.Rmd")

# Or use the batch rendering script
source("vignettes/renderAllVignettest.R")

Package Development

# Load package for development
devtools::load_all()

# Check package
devtools::check()

# Run tests (if available)
devtools::test()

Technology Stack

  • Presentation Framework: xaringan (remark.js-based slides)
  • Output Format: HTML presentations with custom CSS (metropolis theme)
  • Statistical Packages: coin, lme4, lmerTest, multcomp, pwr, asympTest
  • Data Manipulation: tidyverse, dplyr, tidyr, purrr
  • Visualization: ggplot2, ggfortify, GGally, ggbeeswarm
  • Proteomics: MSqRob (from statOmics), limma (Bioconductor)

Vignette Rendering Details

All vignettes use xaringan::moon_reader with:

  • 16:9 aspect ratio
  • metropolis theme
  • GitHub-style code highlighting
  • Incremental slide numbering
  • Custom CSS from trug-ggplot2.css

Important Notes

  • This is an educational package, not a production tool
  • Vignettes are designed as presentation slides, not analysis reports
  • Images are referenced from ../inst/images/ in vignettes
  • Package dependencies include both CRAN and Bioconductor packages (see DESCRIPTION:42-44)