| name | rnaseq-de |
| description | Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing. |
| version | 0.1.0 |
| tags | ["rna-seq","differential expression","bulk","pseudo-bulk","transcriptomics","DESeq2","PyDESeq2","QC","PCA"] |
| trigger_keywords | ["rna-seq","differential expression","bulk RNA","pseudo-bulk","volcano plot","ma plot","count matrix","DESeq2","pydeseq2"] |
| metadata | {"openclaw":{"requires":{"bins":["python3"],"env":[],"config":[]},"always":false,"emoji":"🧬","homepage":"https://github.com/ClawBio/ClawBio","os":["darwin","linux"],"install":[{"kind":"uv","package":"pandas","bins":[]},{"kind":"uv","package":"numpy","bins":[]},{"kind":"uv","package":"matplotlib","bins":[]},{"kind":"uv","package":"scikit-learn","bins":[]}]}} |
🧬 RNA-seq Differential Expression
This skill performs differential expression on bulk RNA-seq or pseudo-bulk count matrices.
Core Capabilities
- Input validation for count matrix and sample metadata
- Pre-DE QC (library size, detected genes, low-count filtering)
- PCA visualisation on normalized expression
- Differential expression from formula + contrast
- Volcano and MA plots
- 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
python rnaseq_de.py \
--counts counts.csv \
--metadata metadata.csv \
--formula "~ batch + condition" \
--contrast "condition,treated,control" \
--output report_dir
Safety
- Local-only processing
- Warn before overwriting existing output
- Report-level disclaimer required
