science by clawbio
🧪 Affinity Proteomics Pipeline clawbio/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.
What it changes View full report → Passed 16 of 19 test cases with the skill, and 4 of 19 without it.
Without skill 23%
With skill 86%
Checks it passed that the model alone missed and 21 more in the full report
14 fixed5 passed either way3 still failing0 broke
Pass-rate lift +64 pp
Tokens +26%
Agent turns 0%
Response time -47% Model gemini-3.6-flashMeasured 8/16/2026 v1 19 of 22 cases passed with skill · 19 comparable
Use this skill Claude Code DecimalAI agent CLI & files
Save it into your project's skills folder. Claude Code picks it up in its next session.
curl -fsSL --create-dirs -o .claude/skills/clawbio-affinity-proteomics/SKILL.md https://app.decimal.ai/s/clawbio-affinity-proteomics/SKILL.md Copy command Copy SKILL.md
Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add clawbio-affinity-proteomics, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"
Linked stays up to date: your agents get the author's new versions automatically.
Editable copy is yours to change; the author's updates won't reach it.
Install linked skill Create editable copy
1 · One-time — install the CLI (
docs ↗ )
$ pip install "decimalai>=0.15"Copy
2 · Get the skill — writes .agents/skills/clawbio-affinity-proteomics/ and pins it in .decimal/skills.lock
$ decimalai skills add clawbio-affinity-proteomicsCopy
Copy link Copy README badge Copy SKILL.md No CLI? Get the same file — curl · raw file $ curl -fsSL --create-dirs -o .claude/skills/clawbio-affinity-proteomics/SKILL.md https://app.decimal.ai/s/clawbio-affinity-proteomics/SKILL.mdCopy
Safety checks: 3 of 3 passed
Code scan Clean Intent Passed Content Clean
Overview Benchmark Contents Activity Versions 1 Ratings 0
See it in action One of 13 test cases the skill fixed. Same model, same prompt, with and without the skill.
Prompt What exact schema identifier string is recorded under workflow_state.state_schema in the JSON output report?
What was checked, without and with the skill Checked Without skill With skill Specifies schema identifier affinity_proteomics.workflow_state.v1.
Show both answers
What's inside The instructions your model reads when the skill loads.
SKILL.md 137 lines single file
🧪 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 conventionsWith it : A single command handles both platforms with correct QC, normalisation, and analysis under a unified interfaceWhy 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
Dual-platform support : Olink NPX (CSV/Parquet) and SomaLogic ADAT under one interfacePlatform-specific QC : Olink (QC_Warning, LOD, sample median) / SomaLogic (RowCheck, ColCheck, normalisation scale factors, MAD outlier filtering)Differential abundance : t-test or Mann-Whitney U with Benjamini-Hochberg FDR correctionVisualisation : Volcano plot, heatmap (top N proteins), PCA plotStructured reporting : Markdown report, result.json, per-protein TSV, reproducibility bundleSkill Action Menu : result.json includes a workflow state plus read-only follow-up actions for compact report cards
Input Formats
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 \
Track record Benchmark 16 / 19
test cases passed, vs 4 / 19 without
Adoption
Users 0
Times used 0 View activity → Safety and source details
SkillSafety ✓ 3 of 3 passed ✓ Code scan 15 of 15 checks clean
0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026
View 15 scanner checks live_secret remote_code_execution reverse_shell data_exfiltration ssrf_metadata agent_snooping anti_refusal destructive_commands obfuscated_unicode unicode_homoglyph opaque_blob suspicious_url tool_overreach trigger_abuse prompt_injection_phrasing
✓ Intent Safe
LLM judge · does the skill do what it claims
✓ Content Clean
LLM judge · policy & harmful-content review
Source Imported License MITImported 8/3/2026Version v1