Agent skill

affinity-proteomics

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeships scriptsNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill affinity-proteomics --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 7
SKILL.md size: 7 KB
Bundled scripts: yes
Version: 0.1.0
Declared author: Reza
Path: skills/clawbio/affinity-proteomics/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

# 🧪 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 protein

What's inside
Steps it walks through
  1. Why This Exists
  2. Core Capabilities
  3. Input Formats
  4. CLI Reference
  5. Demo
  6. Output Structure
  7. Suggested Actions
  8. Dependencies
  9. Safety
  10. Integration with Bio Orchestrator
  11. Citations
Ships with 6 files
  • affinity_proteomics.py
  • example_data/olink_demo_meta.csv
  • example_data/olink_demo_npx.csv
  • requirements.txt
  • tests/__init__.py
  • tests/test_affinity_proteomics.py
Commands it runs
Olink demo
python skills/affinity-proteomics/affinity_proteomics.py \
SomaLogic demo
Real Olink data
Via ClawBio runner
python clawbio.py run affprot --demo --platform olink
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About this skill
What does the affinity-proteomics skill do?

Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill affinity-proteomics --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.

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