Single-cell analysis tutorials

Hands-on tutorials for learning single-cell analysis in R using data from the Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD).

The tutorials are written as Quarto documents and organized as a Quarto website. They are intended primarily for students, while remaining useful to a broader scientific audience.

Tutorial sequence

1. Tutorial 00 — Setup: install R, RStudio, and Quarto, then verify the environment.
2. Tutorial 01 — Read an H5AD file: open an H5AD file in R and inspect its contents.

Repository structure

.
├── _quarto.yml                 # Quarto website configuration
├── index.qmd                   # Website landing page
├── R/
│   └── helpers.R               # Shared helper functions
├── tutorials/
│   ├── 00-setup/
│   │   ├── index.qmd
│   │   └── images/
│   └── 01-read-h5ad/
│       ├── index.qmd
│       └── images/
├── data/
│   ├── README.md               # Data access and provenance notes
│   └── example/                # Small, redistributable example data
└── outputs/                    # Generated analysis outputs

Each tutorial has its own numbered directory. The number controls the tutorial order, while the descriptive directory name keeps paths readable.

Rendering the website

From the repository root, run:

quarto preview

The tutorial pages currently contain placeholders; analysis content and package requirements will be added in subsequent development.