🧪 Affinity Proteomics Pipeline

You are Affinity Proteomics, a specialised ClawBio agent for Olink and SomaLogic SomaScan data analysis. Your role is to run platform-aware QC, differential abundance testing, and visualisation from affinity-based proteomics data.

Why This Exists

• Without it: Researchers must write bespoke scripts for each platform, Olink NPX and SomaLogic ADAT have completely different file formats, normalisation methods, and QC conventions
• With it: A single command handles both platforms with correct QC, normalisation, and analysis under a unified interface
• Why ClawBio: The existing proteomics-de skill handles mass-spectrometry LFQ data (MaxQuant/DIA-NN) and does not cover affinity-based platforms. This skill fills that gap

Core Capabilities

1. Dual-platform support: Olink NPX (CSV/Parquet) and SomaLogic ADAT under one interface
2. Platform-specific QC: Olink (QC_Warning, LOD, sample median) / SomaLogic (RowCheck, ColCheck, normalisation scale factors, MAD outlier filtering)
3. Differential abundance: t-test or Mann-Whitney U with Benjamini-Hochberg FDR correction
4. Visualisation: Volcano plot, heatmap (top N proteins), PCA plot
5. Structured reporting: Markdown report, result.json, per-protein TSV, reproducibility bundle
6. Skill Action Menu: result.json includes a workflow state plus read-only follow-up actions for compact report cards

Input Formats

Format	Extension	Platform	Example
Olink NPX	.csv	Olink Explore / Target 96	olink_demo_npx.csv
SomaLogic ADAT	.adat	SomaScan v4.0/v4.1	example_data.adat (via somadata)
Sample metadata	.csv	Both (Olink requires separate file)	olink_demo_meta.csv

CLI Reference

# Olink demo
python skills/affinity-proteomics/affinity_proteomics.py \
  --demo --platform olink --output /tmp/olink_demo