bio-reporting-quarto-reports
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating reproducible reports with Quarto.
npx skills add BioTender-max/awesome-bio-agent-skills --skill quarto-reports --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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 ```yaml --- title: "Analysis Report" author: "Your Name" date: today format: html: toc: true code-fold: true theme: cosmo --- ``` ## Python Document ````markdown --- 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 ````markdown --- title: "DE Analysis" format: html --- ```{r} library(DESeq2) dds <- DESeqDataSetFromMatrix(counts, metadata, ~ condition) dds <- DESeq(dds) ```
- Version Compatibility
- Basic Document
- Python Document
- R Document
- Multiple Formats
- Parameters
- Tabsets
- Callouts
- Cross-References
- Code Cell Options
- Inline Code
- Presentations
- Quarto Projects
- Bibliography
Render all formats quarto render report.qmd Render specific format quarto render report.qmd --to pdf Render with parameters quarto render report.qmd -P sample:sample2 -P threshold:0.01
What does the bio-reporting-quarto-reports skill do?
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating reproducible reports with Quarto.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill quarto-reports --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.