Affinity Proteomics

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “/affinity-proteomics”

Requirements

• Python 3
• Node.js

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

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

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • pubmed.ncbi.nlm.nih.gov
  • cran.r-project.org
  • pypi.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Affinity Proteomics loads about 1.8k tokens when it runs. Until then it costs about 59 tokens; SKILL.md has 518 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~59

When it runs · the whole SKILL.md, loaded when a task matches

~1.8k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 518 words, ~1,801 tokens.

name

affinity-proteomics

description

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.

license

MIT

metadata.version

0.1.0

metadata.author

Reza

metadata.tags

proteomics, olink, somalogic, somascan, npx, affinity, differential-abundance, biomarker

# 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

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

{
  "workflow_state": {
    "state_schema": "affinity_proteomics.workflow_state.v1",
    "state_id": "sha256:...",
    "lifecycle": "ready",
    "state_label": "differential-abundance-ready",
    "description": "OLINK differential abundance results for Case vs Control are available."
  },
  "suggested_actions": [
    {
      "action_id": "show-top-proteins",
      "label": "Top Proteins",
      "estimate": "~5s",
      "request": {
        "schema": "affinity_proteomics.action_request.v1",
        "action": "top-proteins",
        "state_schema": "affinity_proteomics.workflow_state.v1",
        "state_id": "sha256:...",
        "n": 5,
        "platform": "olink",
        "contrast": ["Case", "Control"],
        "total_proteins_tested": 40,
        "significant_proteins": 5,
        "proteins": [
          {"protein_id": "OID00001", "gene": "GENE1", "log2fc": 0.0, "padj": "0.00e+00"}
        ]
      }
    }
  ]
}

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files in skills/affinity-proteomics of ClawBio/ClawBio.

• SKILL.md
• 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

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

• BioTender-max/awesome-bio-agent-skillsskills/clawbio/affinity-proteomics