r4babs

https://github.com/3mmarand/r4babs

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Repository

https://github.com/3mmaRand/R4BABS/blob/main/

# Data Analysis in R for Becoming a Bioscientist (R4BABS)

R4BABS is a Quarto-powered website that gathers teaching materials for the University of York Biology curriculum. The site renders into the `_site` directory and offers navigation for BABS1, BABS2, BABS4, and the postgraduate course PGT52M.

## Teaching Materials

- **BABS1**  Stage1 module taken by every student. Covers core concepts of scientific computing, types of variables, the role of variables in analysis, and how to use RStudio to organise work and import, summarise, and plot data.
- **BABS2**  Stage1 module building on BABS1. Introduces classical statistics, including the logic of hypothesis testing, confidence intervals, statistical models, two-sample tests, and one- and two-way ANOVA.
- **BABS4**  Stage2 module. Starts with a review of stage1 skills (file types, file systems, working directories, paths, and RStudio Projects) then covers project organisation, working with datasets that have many variables and observations, getting an overview with summaries and distribution plots, and filtering rows and columns. The final three workshops, aimed at Biomedical Science students, teach flow cytometry data analysis.
- **PGT52M**  Postgraduate module revisiting core concepts before progressing through hypothesis testing, regression, ANOVA, and assessment preparation.

## Getting Started

1. **Restore the R environment**
   ```r
   renv::restore()
   ```
   Targets R4.5.0 with Bioconductor3.21 repositories.

2. **Render the site**
   ```bash
   quarto render       # build the entire site
   quarto preview      # serve locally with live reload
   ```

## Continuous Deployment

A GitHub Actions workflow builds and deploys the rendered site to the `gh-pages` branch whenever changes land on `main`.

## Repository Layout

- `_quarto.yml`  project configuration
- `r4babs1/`, `r4babs2/`, `r4babs4/`, `pgt52m/`  module content organised by week
- `renv.lock`, `renv/`  reproducible R package environment
- `CITATION.cff`  citation metadata
- `.github/workflows/`  deployment workflow

## Citation

> Rand, E. *Data Analysis in R for Becoming a Bioscientist* (Version0.1).
> https://3mmarand.github.io/R4BABS/

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