🧪 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

Input Formats

.csv

olink_demo_npx.csv

.adat

example_data.adat

.csv

olink_demo_meta.csv

CLI Reference

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

# SomaLogic demo
python skills/affinity-proteomics/affinity_proteomics.py \
  --demo --platform somascan --output /tmp/soma_demo

# Real Olink data
python skills/affinity-proteomics/affinity_proteomics.py \
  --platform olink --input data.csv --meta samples.csv \
  --group-col Group --contrast "Case,Control" --output results/

# Via ClawBio runner
python clawbio.py run affprot --demo --platform olink

Demo

python clawbio.py run affprot --demo --platform olink

Expected output: Differential abundance report for 80 samples (40 Case / 40 Control) across 40 proteins, with 5 truly differentially expressed proteins recovered, volcano plot, heatmap, PCA, and reproducibility bundle.

Dependencies

Required:

• somadata

  >= 1.2 — SomaLogic ADAT parsing

• scipy

  >= 1.10 — statistical tests

• statsmodels

  >= 0.14 — multiple testing correction

• matplotlib

  >= 3.7 — plotting

• seaborn

  >= 0.13 — heatmaps

• numpy

  >= 1.24 — numerical operations

• pandas

  >= 2.0 — data manipulation

• scikit-learn

  >= 1.3 — PCA dimensionality reduction for sample-level QC plots

Safety

• Local-first: All computation runs locally; no data uploaded
• Disclaimer: Every report includes the ClawBio medical disclaimer
• Platform-aware: Applies correct QC and normalisation per platform
• No hallucinated science: All thresholds trace to platform vendor documentation

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

• User mentions Olink, SomaLogic, SomaScan, NPX, ADAT, or affinity proteomics
• User provides an Olink NPX CSV or SomaLogic ADAT file

Chaining partners:

• proteomics-de

  : Complementary — handles mass-spec LFQ; this skill handles affinity platforms

• diff-visualizer

  : Downstream — enhanced visualisation of differential abundance results

Citations

• Assarsson et al. (2014) — Olink PEA technology
• Gold et al. (2010) — SOMAmer aptamer technology
• OlinkAnalyze — Official Olink R toolkit
• somadata — Python ADAT parser