/rnaseq-de

name: rnaseq-de
description: Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
license: MIT
metadata:
  version: 0.1.0
  tags:
  - rna-seq
  - differential expression
  - bulk
  - pseudo-bulk
  - transcriptomics
  - DESeq2
  - PyDESeq2
  - QC
  - PCA
  openclaw:
    requires:
      bins:
      - python3
    always: false
    emoji: 🧬
    homepage: https://github.com/ClawBio/ClawBio
    os:
    - darwin
    - linux
    install:
    - kind: uv
      package: pandas
    - kind: uv
      package: numpy
    - kind: uv
      package: matplotlib
    - kind: uv
      package: scikit-learn
    trigger_keywords:
    - rna-seq
    - differential expression
    - bulk RNA
    - pseudo-bulk
    - volcano plot
    - ma plot
    - count matrix
    - DESeq2
    - pydeseq2

🧬 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

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