Bioinformatics & Scientific AI Agent Skills 🤖🧬

Agent Skills Standard Total Skills Compatibility CI Test Suite License

An open-source collection of specialized AI Agent Skills, Tool Specifications, and Prompt Protocols for Bioinformatics, Genomics, Structural Biology, Metagenomics, and AI Drug Discovery.

Designed to transform LLM Coding Agents (Cursor, Claude Code CLI, Google Antigravity, OpenAI Codex, Gemini CLI, LangChain) into autonomous, domain-expert AI Scientists.

📋 Available Agent Skills Directory

Skill Name Target Domain Supported Tools & APIs Skill Documentation
scanpy-sc-analyzer Single-Cell Genomics Scanpy, Harmony, AnnData, UMAP skills/scanpy-sc-analyzer/SKILL.md
pydeseq2-bulk-rna Bulk RNA-Seq Transcriptomics PyDESeq2, DESeq2, limma, Volcano Plots skills/pydeseq2-bulk-rna/SKILL.md
alphafold-pocket-evaluator Structural Biology AlphaFold DB, py3Dmol, Biopython, FreeSASA skills/alphafold-pocket-evaluator/SKILL.md
ensembl-vep-variant-annotator Clinical Genomics Ensembl VEP API, ClinVar, Open Targets skills/ensembl-vep-variant-annotator/SKILL.md
rdkit-qsar-pharmacophore AI Drug Discovery RDKit, ECFP4 Fingerprints, LightGBM, SHAP skills/rdkit-qsar-pharmacophore/SKILL.md
pubmed-rag-synthesizer Biomedical AI PubMedBERT, FAISS Vector Search, EUtils skills/pubmed-rag-synthesizer/SKILL.md
nextflow-dsl2-generator Cloud HPC & Workflows Nextflow DSL2, Docker, AWS Batch, SLURM skills/nextflow-dsl2-generator/SKILL.md
gatk4-somatic-variant-caller Somatic Variant Calling GATK4 Mutect2, SAMtools, BCFtools skills/gatk4-somatic-variant-caller/SKILL.md
qiime2-16s-microbiome Metagenomics QIIME2, DADA2, scikit-bio, SILVA skills/qiime2-16s-microbiome/SKILL.md
diffdock-virtual-screener AI Docking & Screening DiffDock, PyTorch, RDKit, AlphaFold skills/diffdock-virtual-screener/SKILL.md
tcga-cibersort-deconv Cancer Microenvironment TCGAbiolinks, CIBERSORT, limma skills/tcga-cibersort-deconv/SKILL.md
card-amr-profiler Microbiology & AMR CARD Database, ResFinder, RGI skills/card-amr-profiler/SKILL.md

🎯 Getting Started & Installation

Option 1: Using npx (Supported Agent Hosts)

Install skills into your agent host in a single command:

npx skills add YuliaNuzhnenko/bioinformatics-agent-skills

Option 2: GitHub CLI (gh skill)

gh skill install YuliaNuzhnenko/bioinformatics-agent-skills

Option 3: Manual Project Configuration (Cursor / Antigravity / Claude Code)

Clone this repository directly into your user or project agent skills directory:

git clone https://github.com/YuliaNuzhnenko/bioinformatics-agent-skills.git ~/.agents/skills/bioinformatics-agent-skills

🖥 Actual Executed Console Output

When running python scan_skills.py locally:

==================================================
 Bioinformatics Agent Skills Validator
==================================================

  [VALID] alphafold-pocket-evaluator     (v1.0.0) - skills\alphafold-pocket-evaluator
  [VALID] card-amr-profiler              (v1.0.0) - skills\card-amr-profiler
  [VALID] diffdock-virtual-screener      (v1.0.0) - skills\diffdock-virtual-screener
  [VALID] ensembl-vep-variant-annotator  (v1.0.0) - skills\ensembl-vep-variant-annotator
  [VALID] gatk4-somatic-variant-caller   (v1.0.0) - skills\gatk4-somatic-variant-caller
  [VALID] nextflow-dsl2-generator        (v1.0.0) - skills\nextflow-dsl2-generator
  [VALID] pubmed-rag-synthesizer         (v1.0.0) - skills\pubmed-rag-synthesizer
  [VALID] pydeseq2-bulk-rna              (v1.0.0) - skills\pydeseq2-bulk-rna
  [VALID] qiime2-16s-microbiome          (v1.0.0) - skills\qiime2-16s-microbiome
  [VALID] rdkit-qsar-pharmacophore       (v1.0.0) - skills\rdkit-qsar-pharmacophore
  [VALID] scanpy-sc-analyzer             (v1.0.0) - skills\scanpy-sc-analyzer
  [VALID] tcga-cibersort-deconv          (v1.0.0) - skills\tcga-cibersort-deconv

Total Valid Skills Processed: 12
 All skills passed schema validation successfully!

🤖 Agent Execution Examples

1. Single-Cell RNA-Seq Workflow

Prompt: "Use scanpy-sc-analyzer skill to filter low-quality cells, run Harmony batch correction, and project UMAP clustering."

2. Clinical VCF Variant Prioritization

Prompt: "Use ensembl-vep-variant-annotator skill to annotate pathogenic driver mutations in sample.vcf.gz and map approved therapies."

🛡 Security & Verification

All Agent Skills in this repository undergo strict schema validation against the canonical Agent Skills specification. No malicious code or hidden telemetry is included.

🤝 Contributing

Contributions from the computational biology and AI research communities are welcome! Feel free to submit Pull Requests with new SKILL.md definitions.

📄 License

Distributed under the MIT License. See LICENSE for details.