Markdown

Plain text with a few symbols for headings, lists, links and code, used in READMEs, Quarto and notebooks

Text

You write	You get
`# Title`, `## Section`, `### Subsection`	headings (one `#` per document, sections from `##`)
a blank line	a new paragraph (a single line break is ignored)
`italic`, `bold`, `~~struck~~`	italic, bold, ~~struck~~
`code`	`code`
`[text](https://quarto.org)`	a link: text
`<https://quarto.org>`	a bare link: https://quarto.org
`![Alt text](results/figure.png)`	an image; the alt text says what it shows
`> A quotation.`	a block quote

Lists and code

- a bullet
- another bullet
  - two spaces in: a sub-bullet

1. numbered
2. list

```bash
pixi run reproduce
```

Leave a blank line before lists, code blocks, tables and headings. Give code blocks a language (bash, python, yaml).

Tables

| Sample     | Generation | Variants |
|------------|-----------:|---------:|
| SRR2589044 |      5,000 |       10 |
| SRR2584866 |     50,000 |      775 |

In the second line, ---: aligns right and :---: centres. Tables made from data belong in code (Quarto), not typed.

What Quarto adds

::: {.callout-note}
A box that draws attention. Also callout-tip, -warning, -important.
:::

See @fig-quality and @tbl-reads.      (cross-references to labelled cells)
As shown by @tenaillon2016.           (a citation from references.bib)

See the Markdown extra and the Quarto cheat sheet.

Official cheat sheets and references

CommonMark quick reference, from the CommonMark project that standardizes Markdown (with a 10-minute tutorial): https://commonmark.org/help/
Quarto, Markdown Basics: https://quarto.org/docs/authoring/markdown-basics.html
GitHub Docs, Basic writing and formatting syntax (Markdown in READMEs, issues and pull requests): https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax