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auto-proteomics

Public OpenClaw skill for low-token routing and downstream analysis of processed DDA LFQ proteomics inputs. Use when the user already has protein-level quantification tables such as MaxQuant-style `proteinGroups.txt` and needs a clear two-group downstream workflow.

skill-install — Terminal

Install via CLI (Recommended)

clawhub install openclaw/skills/skills/billwanttobetop/auto-proteomics
Or

Auto Proteomics

Author: Guo Xuan 郭轩
Contact: [email protected]

auto-proteomics is a public v0.x skill for processed proteomics downstream work.

The current public promise is intentionally narrow:

  • one shipped runnable workflow: dda-lfq-processed
  • one public input family: processed DDA LFQ protein-level tables
  • one public comparison model: group-a vs group-b

Everything else in this repository should be read as routing context, internal prototype, or future scaffold unless a document explicitly marks it as part of the public promise. Presence of a script, schema, or branch document does not mean the route is publicly supported. In particular, dia-quant is intentionally exposed as an internal prototype route for correct routing and contract validation, not as a shipped public workflow.

Use this skill when

  • the user already has processed protein-level quantification output
  • the main table is MaxQuant-like proteinGroups.txt
  • the goal is QC, normalized matrix generation, and two-group differential protein analysis
  • the user wants a low-token, file-driven workflow instead of a long chat-only protocol

Do not use this skill when

  • the user starts from raw spectra and needs search/identification
  • the request is primarily DIA, phosphoproteomics, enrichment, or multi-omics execution
  • the task requires more than one comparison design in the current release
  • the user only wants generic statistics with no proteomics context

Public promise in v0.x

Shipped and supported now:

  • route processed DDA LFQ downstream requests into dda-lfq-processed
  • validate the expected processed-input shape
  • generate matrix, QC, differential tables, report, and manifest outputs

Not promised yet:

  • raw-spectrum search pipelines
  • DIA public execution support
  • phosphoproteomics execution
  • enrichment execution
  • multi-omics execution
  • generalized study-design handling beyond the current two-group path

Internal prototype route available for routing only:

  • dia-quant may be selected only when the request is explicitly about processed DIA quant tables that fit the checked-in DIA contract
  • selecting dia-quant means internal prototype triage, never a public v0.x execution recommendation

Important boundary:

  • non-shipped branches may contain scaffold or prototype execution files for internal framework development
  • smaller models must not treat those files as public runnable recommendations unless a route is explicitly marked shipped

Minimal workflow

  1. Read references/WORKFLOW_INDEX.yaml
  2. If the route is unclear, run scripts/decision/route_proteomics.py
  3. Check that the request fits the public v0.x boundary
  4. Run scripts/workflows/dda_lfq_processed.sh
  5. Use references/ for runtime, onboarding, and development rules

Public runnable entrypoint

Read Full Documentation on GitHub

Metadata

Author@billwanttobetop
Stars4473
Views1
Updated2026-05-01
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Add to Configuration

Paste this into your clawhub.json to enable this plugin.

{
  "plugins": {
    "official-billwanttobetop-auto-proteomics": {
      "enabled": true,
      "auto_update": true
    }
  }
}
Safety NoteClawKit audits metadata but not runtime behavior. Use with caution.

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