rnaseq-de
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
npx skills add BioTender-max/awesome-bio-agent-skills --skill rnaseq-de --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.
# 🧬 RNA-seq Differential Expression This skill performs differential expression on bulk RNA-seq or pseudo-bulk count matrices. ## Core Capabilities 1. Input validation for count matrix and sample metadata 2. Pre-DE QC (library size, detected genes, low-count filtering) 3. PCA visualisation on normalized expression 4. Differential expression from formula + contrast 5. Volcano and MA plots 6. Markdown report with reproducibility files ## Input Contract - Count matrix (`.csv` or `.tsv`): rows are genes, columns are samples, first column is gene identifier - Metadata table (`.csv` or `.tsv`): one row per sample, must include `sample_id` - Formula: e.g. `~ condition` or `~ batch + condition` - Contrast: `factor,numerator,denominator` (e.g. `condition,treated,control`) ## Output Structure ``` rnaseq_de_report/ ├── report.md ├── figures/ │ ├── pca.png │ ├── volcano.png │ └── ma_plot.png ├── tables/ │ ├── qc_summary.csv │ ├── normalized_counts.csv │ └── de_results.csv └── reproducibility/ ├── commands.sh ├── environment.yml └── checksums.sha256 ``` ## Usage ```bash python rnaseq_de.py \ --counts counts.csv \ --metadata metadata.csv \ --formula "~ batch + condition" \ --contrast "condition
- Core Capabilities
- Input Contract
- Output Structure
- Usage
- Safety
python rnaseq_de.py \
What does the rnaseq-de skill do?
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill rnaseq-de --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.