bio-reporting-quarto-reports

Version Compatibility

Reference examples tested with: Quarto 1.4+, DESeq2 1.42+, ggplot2 3.5+, matplotlib 3.8+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Quarto Reports

"Create a Quarto analysis report" → Write reproducible documents mixing code (Python/R), narrative, and figures that render to HTML/PDF/Word.

• CLI: quarto render report.qmd --to html

Basic Document

---
title: "Analysis Report"
author: "Your Name"
date: today
format:
  html:
    toc: true
    code-fold: true
    theme: cosmo
---

Python Document

---
title: "scRNA-seq Analysis"
format: html
jupyter: python3
---

```{python}
import scanpy as sc
import matplotlib.pyplot as plt

adata = sc.read_h5ad('data.h5ad')
sc.pl.umap(adata, color='leiden')
```

R Document

---
title: "DE Analysis"
format: html
---

```{r}
library(DESeq2)
dds <- DESeqDataSetFromMatrix(counts, metadata, ~ condition)
dds <- DESeq(dds)
```

Multiple Formats

---
title: "Multi-format Report"
format:
  html:
    toc: true
  pdf:
    documentclass: article
  docx:
    reference-doc: template.docx
---

# Render all formats
quarto render report.qmd

# Render specific format
quarto render report.qmd --to pdf

Parameters

---
title: "Parameterized Report"
params:
  sample: "sample1"
  threshold: 0.05
---

# Render with parameters
quarto render report.qmd -P sample:sample2 -P threshold:0.01

Tabsets

::: {.panel-tabset}

## PCA
```{r}
plotPCA(vsd)
```

## Heatmap
```{r}
pheatmap(mat)
```

:::

Callouts

::: {.callout-note}
This is an important note about the analysis.
:::

::: {.callout-warning}
Check your input data format before proceeding.
:::

::: {.callout-tip}
Use caching for long computations.
:::