bio-reporting-rmarkdown-reports
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.
npx skills add BioTender-max/awesome-bio-agent-skills --skill rmarkdown-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: rmarkdown 2.25+, knitr 1.45+, DESeq2 1.42+, ggplot2 3.5+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # R Markdown Reports **"Create an R Markdown report"** → Write reproducible R-based documents combining code chunks, results, and narrative that render to HTML/PDF/Word. - R: `rmarkdown::render('report.Rmd')`, or Knit button in RStudio ## Basic Document Structure ```yaml --- title: "RNA-seq Analysis Report" author: "Your Name" date: "`r Sys.Date()`" output: html_document: toc: true toc_float: true code_folding: hide theme: cosmo --- ``` ## Setup Chunk ````r ```{r setup, include=FALSE} knitr::opts_chunk$set( echo = TRUE, message = FALSE, warning = FALSE, fig.width = 10, fig.height = 6, fig.align = 'center' ) library(tidyverse) library(DESeq2) library(pheatmap) ``` ```` ## Code Chunk Options ````r ```{r analysis, echo=TRUE, results='hide'} # echo: show code # resu
- Version Compatibility
- Basic Document Structure
- Setup Chunk
- Code Chunk Options
- Parameterized Reports
- Tables
- Figures
- Inline Code
- Child Documents
- PDF Output
- HTML with Tabs
- Caching Long Computations
- Custom CSS
- Complete Report Template
What does the bio-reporting-rmarkdown-reports skill do?
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill rmarkdown-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.