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LLMs-Universal-Life-Science-and-Clinical-Skills- proteomics-enrichment

install
source · Clone the upstream repo
git clone https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- "$T" && mkdir -p ~/.claude/skills && cp -r "$T/Skills/Proteomics/proteomics-enrichment" ~/.claude/skills/mdbabumiamssm-llms-universal-life-science-and-clinical-skills-proteomics-enrichm && rm -rf "$T"
manifest: Skills/Proteomics/proteomics-enrichment/SKILL.md
tags
#proteomics#enrichment#pathway#STRING#g:Profiler
source content

🗺️ Proteomics Enrichment

Pathway, network, and Gene Ontology enrichment analysis for proteomics data.

CLI Reference

python omicsclaw.py run prot-enrichment --demo
python omicsclaw.py run prot-enrichment --input <proteins.csv> --output <dir>

Parameters

ParameterDefaultDescription
--method
ora
ora or gsea
--species
human
Species

Why This Exists

  • Without it: A list of 500 significant proteins is biologically impossible to interpret
  • With it: Algorithms collapse hundreds of targets into 5 or 10 meaningful biological pathways
  • Why OmicsClaw: Runs fast local enrichment caches utilizing multiple ontologies simultaneously

Workflow

  1. Calculate: Map Uniprot IDs to Gene Symbols or Entrez.
  2. Execute: Hypergeometric tests over known Kegg/GO definitions.
  3. Assess: Perform FDR multiple testing adjustments.
  4. Generate: Output structural network graphs.
  5. Report: Tabulate key functionally enriched terms.

Example Queries

  • "Perform GO enrichment on these significant proteins using STRING"
  • "Run g:Profiler on this list of genes"

Output Structure

output_directory/
├── report.md
├── result.json
├── pathways.csv
├── figures/
│   └── enrichment_dotplot.png
├── tables/
│   └── top_pathways.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    └── checksums.sha256

Safety

  • Local-first: Strict offline processing without external upload.
  • Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
  • Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

  • Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

  • differential-abundance
    — Upstream source of significant proteins

Citations