OpenClaw-Medical-Skills

The largest open-source medical AI skills library for OpenClaw🦞.

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Python
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2026/8/23
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⚠️ 第三方软件声明

本 Skill 为第三方开源软件,独立托管于 GitHub。SkillTip 仅为信息目录,不控制或维护底层仓库。所显示的安全检查为自动化且范围有限,安装前请自行审查源码。

阅读服务条款

安装

添加到你的 Claude Code skills 目录:

# Add to your Claude Code skills
git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills

快速入门

使用 OpenClaw-Medical-Skills 等 Skills 的指南。

安全报告

已验证

上次扫描:—

{
  "status": "PASSED",
  "issues": []
}

README.md

OpenClaw Medical Skills

GitHub Stars GitHub Forks GitHub Issues Skills Count License Platform

The largest open-source medical AI skill library for OpenClaw.

869 curated skills · Clinical · Genomics · Drug Discovery · Bioinformatics · Medical Devices

English | 中文


What Is This?

OpenClaw Medical Skills is a curated collection of 869 AI agent skills covering the full spectrum of biomedical and clinical research. These skills are designed for OpenClaw / NanoClaw — Claude-based personal AI assistant frameworks — and transform a general-purpose AI agent into a powerful medical and scientific research companion.

Each skill is a self-contained module (a SKILL.md file) that:

  • Teaches the agent specialized domain knowledge and workflows
  • Connects to real databases, APIs, and computational tools
  • Produces structured, clinically or scientifically relevant outputs

We benefit from the open-source community. The full collection of resources can be found here: Awesome LLM Resources

Why This Collection Matters

Without SkillsWith OpenClaw Medical Skills
Generic AI responses about medicineReal PubMed / ClinicalTrials.gov / FDA queries
No bioinformatics capabilityRNA-seq, scRNA-seq, GWAS, variant calling pipelines
No drug intelligenceChEMBL, DrugBank, DDI prediction, pharmacovigilance
No clinical documentationSOAP notes, discharge summaries, prior auth decisions
No genomics supportVCF annotation, ACMG classification, PRS calculation
No regulatory guidanceFDA, CE mark, IEC 62304, ISO 14971 compliance

This collection aggregates skills from 12+ open-source skill repositories spanning academic research tools, clinical workflows, regulatory frameworks, and cutting-edge AI-driven protein design — giving your AI agent capabilities comparable to a team of specialized research scientists.


Installation

Requirements

  • OpenClaw installed and running, or NanoClaw as an alternative
  • Git (for cloning this repo)

For OpenClaw Users

OpenClaw loads skills from two locations:

PriorityPathScope
High<workspace>/skills/Per-workspace (recommended)
Low~/.openclaw/skills/Global, shared across all agents

Method 1 — Clone and Copy (Recommended)

# Clone this repository (skills only — skips large data files)
git clone --depth=1 --no-checkout https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git
cd OpenClaw-Medical-Skills
git sparse-checkout init --cone
git sparse-checkout set skills
git checkout main

# Install to your workspace skills directory
cp -r skills/* <your-workspace>/skills/

# Or install globally (available to all agents)
cp -r skills/* ~/.openclaw/skills/

Note: Some skills bundle large data files (databases, datasets). The sparse-checkout method above avoids downloading them. If you need the full repo including all data, install Git LFS first, then run git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git.

Skills are picked up automatically on the next session. No restart needed.

Method 2 — OpenClaw CLI

If you use the OpenClaw plugin registry, you can search and install individual skills from there. For bulk install from this collection, Method 1 is faster.

openclaw plugins install <skill-slug>    # install a single skill
openclaw plugins update                  # update all installed skills

Method 3 — Configure Extra Directories

To point OpenClaw at a cloned copy of this repo permanently, add it to ~/.openclaw/openclaw.json:

{
  "plugins": {
    "local": ["/path/to/OpenClaw-Medical-Skills"]
  }
}

This mounts the entire collection without copying files.

Method 4 — Install Selected Skills Only

Pick skills relevant to your domain:

# Example: clinical + drug discovery stack
SKILLS=(
  "clinical-reports"
  "tooluniverse-drug-research"
  "tooluniverse-pharmacovigilance"
  "clinicaltrials-database"
  "biomedical-search"
  "tooluniverse-drug-drug-interaction"
)

for skill in "${SKILLS[@]}"; do
  cp -r OpenClaw-Medical-Skills/skills/$skill ~/.openclaw/skills/
done

For NanoClaw Users

NanoClaw loads skills into agent containers at startup from container/skills/.

# Clone and copy into NanoClaw container skills directory
git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git
cp -r OpenClaw-Medical-Skills/skills/* /path/to/nanoclaw/container/skills/

# Rebuild the container to apply
cd /path/to/nanoclaw
./container/build.sh

Verification

After installation, ask your agent:

What medical and clinical skills do you have available?

Your agent should list the installed skills with their capabilities.


Skills Overview

CategoryCountHighlights
General & Core10Browser/search, document tools, and developer workflow utilities
Medical & Clinical119Clinical reports, CDS, oncology, imaging, and healthcare AI
Scientific Databases43Genomics/protein/drug databases and biomedical knowledge retrieval
Bioinformatics (gptomics)239Variant analysis, sequencing QC, DE, pathways, single-cell, and epigenomics
Omics & Computational Biology59Single-cell/spatial, proteomics, cheminformatics, and protein design tools
ClawBio Pipelines21Orchestration pipelines for scRNA, GWAS, ancestry, and structural workflows
BioOS Extended Suite285Extended agent suite for oncology, immunology, clinical AI, and infrastructure
Data Science & Tools93Statistics, visualization, automation, simulation, and scientific tooling
Total869

Table of Contents

General & Core

Medical & Clinical

Scientific Databases

Bioinformatics (gptomics bio-* suite)

Omics & Computational Biology

ClawBio Pipelines

BioOS Extended Suite

Data Science & Tools


Skills List

🧰 General & Core

Expand/Collapse this category

General Tools

Click to expand skill list
SkillDescription
agent-browserBrowse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test web pages. Use whenever a browser would be useful.
find-skillsHelps users discover and install agent skills when they ask questions like "how do I do X", "find a skill for X", "is there a skill that can...", or express interest in extending capabilities.
multi-search-engineMulti search engine integration with 17 engines (8 CN + 9 Global). Supports Baidu, Bing, 360, Sogou, WeChat, Google, DuckDuckGo, WolframAlpha and more. Supports advanced operators, time filters, site search. No API keys required.
wikipedia-searchSearch and fetch structured content from Wikipedia using the MediaWiki API for reliable, encyclopedic information. Supports multi-language queries.
deep-researchExecute autonomous multi-step deep research on any topic. Searches multiple sources, reads full content, synthesizes findings, and produces a structured report. Use for comprehensive research, literature reviews, competitive analysis, or topic deep-dives.
pdfComprehensive PDF toolkit — extract text and tables, create new PDFs, merge/split documents, handle forms, OCR scanned PDFs. Use when working with any .pdf file.
docxCreate, edit, and analyze Word documents (.docx). Supports tracked changes, comments, formatting preservation, and text extraction. Use for drafting, redlining, or extracting content from Word files.
xlsxSpreadsheet creation, editing, and analysis. Supports formulas, formatting, data analysis, and visualization. Use for any .xlsx, .xlsm, .csv, or .tsv task.
pptxPresentation creation, editing, and analysis. Supports layouts, speaker notes, templates, and design. Use for any .pptx file.
doc-coauthoringGuide users through a structured workflow for co-authoring documentation. Use when writing documentation, proposals, technical specs, decision docs, or similar structured content.

🏥 Medical & Clinical

Expand/Collapse this category

Medical Tools

Click to expand skill list
SkillDescription
pubmed-searchSearch PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies.
medical-research-toolkitQuery 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research. Access ChEMBL, PubMed, ClinicalTrials.gov, OpenTargets, OpenFDA, OMIM, Reactome, KEGG, UniProt, and more through a unified MCP endpoint.
medical-specialty-briefsGenerate daily or on-demand medical research briefs for any medical specialty. Searches latest research from top-tier journals (NEJM, Lancet, JAMA, BMJ, Nature Medicine), delivers concise summaries with 1-sentence takeaways and direct links. Use when user asks for medical news, research updates, or specialty-specific updates (endocrinology, cardiology, oncology, neurology, etc.).
usmlePrepare for US medical licensing exams with progress tracking, weak area analysis, question bank management, and residency match planning. Covers Step 1/2 CK/Step 3, IMG-specific guidance, score prediction, and wellbeing support.
medical-entity-extractorExtract medical entities (symptoms, medications, lab values, diagnoses) from patient messages.
patiently-aiSimplifies medical documents for patients. Takes doctor's letters, test results, prescriptions, discharge summaries, and clinical notes and explains them in clear, personalised language.
biomedical-searchComplete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.
medical-imaging-reviewWrite comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on imaging topics.
fhir-developer-skillFHIR API development guide for building healthcare endpoints (Patient, Observation, Encounter, Condition, MedicationRequest). Use when developing or integrating FHIR REST APIs.
clinical-trial-protocol-skillGenerate clinical trial protocols for medical devices or drugs. Use when designing clinical studies, creating FDA submission documentation, or developing protocols for investigational products.
prior-auth-review-skillAutomate payer review of prior authorization (PA) requests. Assesses medical necessity, validates against coverage policies, and generates PA decisions.
clinical-reportsWrite comprehensive clinical reports — case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, CSR), and patient documentation (SOAP, H&P, discharge summaries). HIPAA/FDA/ICH-GCP compliant.
clinicaltrials-databaseQuery ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data for clinical research and patient matching.
clinical-decision-supportGenerate clinical decision support (CDS) documents for pharmaceutical and clinical research — patient cohort analyses, treatment recommendation reports with GRADE evidence grading, biomarker integration, and statistical outputs (hazard ratios, survival curves).
tooluniverse-clinical-trial-designStrategic clinical trial design feasibility assessment. Evaluates patient population sizing, biomarker prevalence, endpoint selection, comparator analysis, safety monitoring, and regulatory pathways. Use when planning Phase 1/2 trials or assessing trial feasibility.
tooluniverse-disease-researchGenerate comprehensive disease research reports covering epidemiology, mechanisms, diagnostics, treatments, and ongoing trials. Use when asking about diseases, syndromes, or needing systematic disease analysis.
tooluniverse-literature-deep-researchDeep literature research with target disambiguation, evidence grading, and structured theme extraction. Resolves gene/protein IDs, identifies synonyms, synthesizes biological models, and generates testable hypotheses. Use for thorough literature reviews or target profiles.
tooluniverse-clinical-guidelinesSearch and retrieve clinical practice guidelines from 12+ sources (NICE, WHO, ADA, AHA/ACC, NCCN, SIGN, CPIC, etc.). Covers cardiology, oncology, diabetes, pharmacogenomics, and more. Use when asking about treatment recommendations or standard of care.
tooluniverse-drug-researchComprehensive drug research reports covering identity, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET. Use for drug profiling, safety assessment, or clinical development research.
tooluniverse-drug-repurposingIdentify drug repurposing candidates using target-based, compound-based, and disease-driven strategies. Finds new indications for approved drugs by analyzing targets, bioactivity, and safety profiles.
tooluniverse-drug-drug-interactionDrug-drug interaction prediction and risk assessment. Analyzes CYP450/transporter mechanisms, severity classification, and provides management strategies. Supports polypharmacy analysis (3+ drugs) and alternative drug recommendations.
tooluniverse-rare-disease-diagnosisDifferential diagnosis for rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, and interprets variants of uncertain significance.
tooluniverse-pharmacovigilanceAnalyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates PRR/ROR, identifies serious adverse events, and assesses pharmacogenomic risk.
tooluniverse-clinical-trial-matchingPatient-to-trial matching for precision medicine and oncology. Ranks trials from ClinicalTrials.gov by molecular eligibility, clinical criteria, biomarker alignment, and geographic feasibility with a quantitative Trial Match Score (0-100).
literature-reviewSystematic literature reviews across multiple databases (PubMed, arXiv, bioRxiv, Semantic Scholar). Produces professionally formatted reports with verified citations in APA, Nature, Vancouver styles.
tooluniverse-precision-oncologyActionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, clinical trials, and resistance mechanisms.
tooluniverse-cancer-variant-interpretationClinical interpretation of somatic mutations in cancer. Given gene+variant (e.g., EGFR L858R, BRAF V600E), assesses oncogenicity, therapeutic implications, and trial eligibility.
tooluniverse-variant-analysisProduction-ready VCF processing, variant annotation, and mutation analysis. Parses VCF files, annotates with ClinVar/gnomAD/COSMIC, and interprets clinical significance.
tooluniverse-variant-interpretationSystematic clinical variant interpretation from raw calls to ACMG-classified recommendations. Aggregates evidence from ClinVar, gnomAD, literature, and population databases.
tooluniverse-structural-variant-analysisComprehensive structural variant (SV/CNV) analysis for clinical genomics. Classifies SVs, assesses pathogenicity, and interprets copy number alterations.
tooluniverse-polygenic-risk-scoreBuild and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles and interprets PRS percentiles.
tooluniverse-precision-medicine-stratificationPatient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Identifies treatment-relevant subgroups and biomarker-driven therapy options.
tooluniverse-gwas-trait-to-geneDiscover genes associated with diseases and traits using GWAS Catalog (500k+ associations) and Open Targets Genetics locus-to-gene predictions.
tooluniverse-gwas-drug-discoveryTransform GWAS signals into drug targets and repurposing opportunities. Performs locus-to-gene mapping, druggability assessment, and existing drug identification.
tooluniverse-gwas-study-explorerCompare GWAS studies and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics for cross-study meta-analysis.
tooluniverse-gwas-finemappingIdentify and prioritize causal variants at GWAS loci using statistical fine-mapping. Computes posterior probabilities and credible sets for causal variant identification.
tooluniverse-gwas-snp-interpretationInterpret SNPs from GWAS studies by aggregating evidence from GWAS Catalog, Open Targets Genetics, and ClinVar. Retrieves variant-trait associations and functional annotations.
tooluniverse-phylogeneticsPhylogenetics and sequence analysis — alignment processing, evolutionary tree construction, and evolutionary metrics for pathogens or species.
tooluniverse-epigenomicsEpigenomics data processing — methylation array analysis (CpG filtering, differential methylation), chromatin accessibility, and histone modification analysis.
tooluniverse-rnaseq-deseq2RNA-seq differential expression analysis using PyDESeq2. Performs normalization, dispersion estimation, Wald testing, LFC shrinkage, and pathway enrichment.
tooluniverse-single-cellSingle-cell RNA-seq analysis using scanpy. Performs QC, normalization, PCA, UMAP, Leiden clustering, trajectory analysis, and cell type annotation.
tooluniverse-spatial-transcriptomicsSpatial transcriptomics data analysis — maps gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, and Slide-seq platforms.
tooluniverse-spatial-omics-analysisComputational analysis for spatial multi-omics data integration — spatially variable genes, domain annotation, and tissue-resolved omics.
tooluniverse-proteomics-analysisMass spectrometry proteomics analysis — protein quantification, differential expression, PTMs, and protein-protein interaction network construction.
tooluniverse-metabolomicsMetabolomics research — identifies metabolites and searches databases (HMDB 220k+ metabolites, MetaboLights, Metabolomics Workbench).
tooluniverse-metabolomics-analysisMetabolomics data analysis — metabolite identification, quantification, pathway analysis, and metabolic flux from LC-MS, GC-MS, or NMR data.
tooluniverse-multi-omics-integrationIntegrate transcriptomics, proteomics, epigenomics, genomics, and metabolomics for systems biology and precision medicine.
tooluniverse-multiomic-disease-characterizationSystems-level disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers.
tooluniverse-expression-data-retrievalRetrieve gene expression and omics datasets from ArrayExpress and BioStudies with quality assessment and structured reports.
tooluniverse-gene-enrichmentGene enrichment and pathway analysis using gseapy, PANTHER, STRING, Reactome. Supports GO enrichment, KEGG pathways, and 40+ ToolUniverse tools.
tooluniverse-systems-biologySystems biology and pathway analysis using Reactome, KEGG, WikiPathways, Pathway Commons, and BioModels. Network modeling and pathway simulation.
tooluniverse-protein-interactionsProtein-protein interaction network analysis using STRING, BioGRID, and SASBDB. Maps interaction networks with confidence scores and functional modules.
tooluniverse-protein-structure-retrievalRetrieve protein structure data from RCSB PDB, PDBe, and AlphaFold with quality assessment and comprehensive structural profiles.
tooluniverse-protein-therapeutic-designDesign novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design — RFdiffusion, ProteinMPNN, and ESM.
tooluniverse-antibody-engineeringAntibody engineering and optimization for therapeutics — humanization, affinity maturation, developability assessment, and immunogenicity prediction.
tooluniverse-immune-repertoire-analysisTCR/BCR repertoire analysis from sequencing data — clonality, diversity, V(D)J gene usage, clonal expansion, and antigen specificity prediction.
tooluniverse-immunotherapy-response-predictionPredict patient response to immune checkpoint inhibitors using multi-biomarker integration — TMB, MSI, PD-L1, TIL signatures, and HLA typing.
tooluniverse-infectious-diseasePathogen characterization and drug repurposing for infectious disease outbreaks. Identifies taxonomy, essential proteins, structural targets, and treatment options.
tooluniverse-crispr-screen-analysisCRISPR screen analysis for functional genomics — pooled or arrayed screens (knockout/activation/interference) to identify essential genes and hits.
tooluniverse-target-researchComprehensive biological target intelligence — protein info, structure, interactions, pathways, expression, variant landscape, and drug pipeline.
tooluniverse-network-pharmacologyCompound-target-disease network analysis for drug repurposing, polypharmacology discovery, and systems pharmacology.
tooluniverse-statistical-modelingStatistical modeling on biomedical datasets — linear/logistic regression, mixed-effects models, survival analysis, and Bayesian methods.
tooluniverse-image-analysisBiomedical microscopy image analysis — colony morphometry, cell counting, fluorescence quantification, and statistical comparison of imaging data.
literature-searchComprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv using natural language queries powered by Valyu semantic search.
medrxiv-searchSearch medRxiv medical preprints with natural language queries powered by Valyu semantic search.
clinical-trials-searchSearch ClinicalTrials.gov with natural language queries — find trials by condition, enrollment status, and outcomes via Valyu.
drug-discovery-searchEnd-to-end drug discovery platform combining ChEMBL, DrugBank, targets, and FDA labels via natural language Valyu search.
drug-labels-searchSearch FDA drug labels with natural language queries — indications, dosing, and safety data via Valyu.
chembl-searchSearch ChEMBL bioactive molecules database — compounds, assay data, and bioactivity via Valyu semantic search.
open-targets-searchSearch Open Targets drug-disease associations and target validation via Valyu semantic search.
patents-searchSearch global patents with natural language queries — prior art, patent landscapes, and innovation tracking via Valyu.
drugbank-searchSearch DrugBank comprehensive drug database — mechanisms, interactions, and safety data via Valyu semantic search.
arxiv-searchSearch arXiv preprints (biology, medicine, AI) using natural language queries powered by Valyu semantic search.
gwas-databaseQuery NHGRI-EBI GWAS Catalog for SNP-trait associations by rs ID, disease/trait, or gene. Retrieve p-values and summary statistics for genetic epidemiology.
scikit-survivalSurvival analysis and time-to-event modeling in Python — Kaplan-Meier, Cox regression, log-rank tests, and censored data handling using scikit-survival.

Drug Safety & Chemical Biology

Click to expand skill list
SkillDescription
tooluniverse-adverse-event-detectionDetect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, ROR, IC), and biomedical evidence. Generates quantitative safety signal scores (0-100).
tooluniverse-binder-discoveryDiscover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibility.
tooluniverse-chemical-compound-retrievalRetrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Comprehensive compound profiles with identifiers, properties, bioactivity.
tooluniverse-chemical-safetyComprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions.
tooluniverse-drug-target-validationComputational validation of drug targets across 10 dimensions: disambiguation, disease association, druggability, chemical matter, clinical precedent, safety, and expression evidence.
tooluniverse-sequence-retrievalRetrieve biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.

Medical Imaging & Pathology

Click to expand skill list
SkillDescription
pydicomPython library for working with DICOM medical imaging files. Reading, writing, modifying DICOM data, extracting pixel data, handling metadata and multi-frame files.
histolabDigital pathology image processing toolkit for whole slide images (WSI). Process H&E or IHC stained tissue images, extract tiles from gigapixel slides.
pathmlComputational pathology toolkit for analyzing WSI and multiparametric imaging data. H&E stained images, multiplex immunofluorescence, spatial omics integration.
omero-integrationMicroscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, for high-content screening workflows.
neurokit2Comprehensive biosignal processing: ECG, EEG, EDA, RSP, PPG, EMG, EOG signals. Cardiovascular signal analysis, neurophysiology, and physiological data processing.
neuropixels-analysisNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, for neuroscience research.

Healthcare ML & Clinical AI

Click to expand skill list
SkillDescription
pyhealthComprehensive healthcare AI toolkit for developing ML models with clinical data (EHR, claims). Task definition API, model training, evaluation for clinical NLP and prediction.
scikit-learnMachine learning in Python: supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning.
transformersPre-trained transformer models for NLP, computer vision, audio, and multimodal tasks. Text generation, classification, question answering, and biomedical NLP (BioBERT, ClinicalBERT).
shapModel interpretability using SHAP (SHapley Additive exPlanations). Explain ML model predictions, compute feature importance, generate SHAP plots for biomedical models.
umap-learnUMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), for high-dimensional omics data.

Health & Wellness Analytics

Click to expand skill list
SkillDescription
nutrition-analyzerComprehensive nutrition analysis: macro/micronutrient tracking, dietary assessment, meal planning, food data lookup, and nutritional recommendations.
mental-health-analyzerMental health data analysis: mood tracking, symptom patterns, PHQ/GAD scoring, behavioral insights, and wellness recommendations.
sleep-analyzerSleep quality analysis: sleep stages, duration, efficiency metrics, circadian rhythm assessment, and sleep hygiene recommendations.
rehabilitation-analyzerRehabilitation progress tracking: functional assessments, exercise programs, recovery milestones, and outcome measurement for physical/occupational therapy.
fitness-analyzerFitness performance analysis: exercise tracking, strength/cardio metrics, training load, VO2max estimation, and periodization planning.
health-trend-analyzerLongitudinal health trend analysis: vital sign tracking, biomarker trends, risk factor monitoring, and predictive health insights.
weightloss-analyzerWeight management analytics: caloric balance, body composition tracking, progress monitoring, and evidence-based weight loss strategies.
goal-analyzerHealth goal tracking and analysis: SMART goal setting, progress metrics, habit formation, and motivational insights for wellness objectives.
occupational-health-analyzerOccupational health assessment: workplace ergonomics, exposure risk, work-related illness surveillance, and return-to-work planning.
travel-health-analyzerTravel medicine: destination health risks, vaccination requirements, malaria prophylaxis, altitude sickness, and traveler health preparation.
family-health-analyzerFamily health management: pediatric milestones, family medical history, preventive screening schedules, and multigenerational health tracking.
tcm-constitution-analyzerTraditional Chinese Medicine constitution analysis: TCM body type assessment, pattern differentiation, herbal recommendations, and lifestyle guidance.
emergency-cardGenerate emergency medical information cards with critical health data, medications, allergies, and emergency contacts for patient safety.
ai-analyzerAI-powered comprehensive health data interpretation combining multiple biomarkers and health metrics for holistic wellness assessment.
wellally-techTechnical framework for WellAlly health analytics platform: integration patterns, data pipelines, and health AI infrastructure.

Mental Health & Crisis Intervention

Click to expand skill list
SkillDescription
crisis-detection-intervention-aiDetect crisis signals using NLP and mental health sentiment analysis. Implements suicide ideation detection, automated escalation, and crisis resource integration for mental health apps and recovery platforms.
crisis-response-protocolHandle mental health crisis situations safely: crisis detection, safety protocols, emergency escalation, suicide prevention, and hotline integration for AI coaching applications.
hipaa-complianceEnsure HIPAA compliance when handling PHI. Audit logging, data access controls, security event tracking, and compliance verification for health data applications.
clinical-diagnostic-reasoningIdentify and counteract cognitive biases in medical decision-making through systematic error analysis, differential diagnosis frameworks, and clinical judgment improvement.
speech-pathology-aiAI-powered speech-language pathology: phoneme analysis, articulation visualization, voice disorder assessment, fluency intervention, AAC, and stuttering treatment support.
hrv-alexithymia-expertHeart rate variability biometrics and emotional awareness training. HRV analysis, interoception training, biofeedback, vagal tone assessment, and autonomic nervous system evaluation.
adhd-daily-plannerADHD-optimized daily planning: time-blind friendly scheduling, executive function support, dopamine-aware task design, and neurodivergent-friendly productivity systems.
grief-companionCompassionate bereavement support, memorial creation, grief education, and healing journey guidance through the non-linear path of loss.
jungian-psychologistJungian analytical psychology: shadow work, archetypal analysis, dream interpretation, active imagination, addiction/recovery through depth psychology lens, and individuation process.
modern-drug-rehab-computerComprehensive addiction recovery knowledge system: evidence-based treatment (CBT, DBT, MI, EMDR, MAT), recovery resources, crisis intervention, and family systems for rehab environments.
recovery-community-moderatorTrauma-informed AI moderation for addiction recovery communities: harm reduction, 12-step traditions, conflict detection, and crisis post identification.

Medical Device & Regulatory

Click to expand skill list
SkillDescription
iso-13485-certificationComprehensive toolkit for ISO 13485 QMS documentation for medical devices: gap analysis, Quality Manuals, procedures, Medical Device Files. Covers FDA QMSR, EU MDR compliance.

🗂️ Scientific Databases

Expand/Collapse this category

Scientific Databases (Genomics & Variants)

Click to expand skill list
SkillDescription
clinvar-databaseQuery NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
clinpgx-databaseAccess ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
cosmic-databaseAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
ensembl-databaseQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
gene-databaseQuery NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
geo-databaseAccess NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
ena-databaseAccess European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines.
ggetCLI/Python toolkit for rapid bioinformatics queries with access to 20+ databases: Ensembl, UniProt, AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, BLAST, and more.
pysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Scientific Databases (Proteins, Pathways & Drugs)

Click to expand skill list
SkillDescription
alphafold-databaseAccess AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
pdb-databaseAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.
uniprot-databaseDirect REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For multi-database workflows, prefer bioservices (unified interface to 40+ services).
string-databaseQuery STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
kegg-databaseDirect REST API access to KEGG (academic use). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion.
reactome-databaseQuery Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology.
brenda-databaseAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, substrate-specific enzyme info for biochemical research.
hmdb-databaseAccess Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics.
metabolomics-workbench-databaseAccess NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, for metabolomics and biomarker discovery.
pubchem-databaseQuery PubChem via PUG-REST API (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
chembl-databaseQuery ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, for medicinal chemistry.
drugbank-databaseAccess comprehensive drug information from DrugBank including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data.
zinc-databaseAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening.
opentargets-databaseQuery Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
fda-databaseQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis.
pubmed-databaseDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management.
openalex-databaseQuery and analyze scholarly literature using the OpenAlex database. Search for academic papers, analyze research trends, find works by authors or institutions.
biorxiv-databaseSearch bioRxiv preprint server by keywords, authors, date ranges, or categories, retrieving paper metadata for life sciences preprint discovery.
bioservicesPrimary Python tool for 40+ bioinformatics services. Unified API for UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO — preferred for multi-database workflows.
uspto-databaseAccess USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, for IP analysis and prior art searches.

Cancer Genomics Databases

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SkillDescription
cbioportal-databaseQuery cBioPortal for cancer genomics: somatic mutations, copy number, gene expression, and survival data across hundreds of cancer studies. Cancer target validation, oncogene analysis, and patient-level genomic profiling.
depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity, and gene effect profiles. Identify cancer-specific vulnerabilities and synthetic lethal interactions.
imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons. Access radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required.

Genomic & Molecular Databases

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SkillDescription
bindingdb-databaseQuery BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Drug discovery, lead optimization, polypharmacology, and SAR studies.
gnomad-databaseQuery gnomAD for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Variant pathogenicity interpretation and rare disease genetics.
gtex-databaseQuery GTEx for tissue-specific gene expression, eQTLs, and sQTLs. Link GWAS variants to gene regulation and interpret non-coding variant effects.
interpro-databaseQuery InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, and 11+ databases for protein function prediction.
jaspar-databaseQuery JASPAR for transcription factor binding site profiles (PWMs/PFMs). Regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.
monarch-databaseQuery the Monarch Initiative knowledge graph for disease-gene-phenotype associations. Integrates OMIM, ORPHANET, HPO, ClinVar for rare disease gene discovery.
tiledbvcfScalable VCF/BCF ingestion, storage, and parallel queries using TileDB for population genomics at scale.

Structural Biology & Drug Discovery

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SkillDescription
molecular-dynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Protein/small molecule systems, force fields, energy minimization, RMSD/RMSF analysis, free energy surfaces.
glycoengineeringAnalyze and engineer protein glycosylation. Predict N/O-glycosylation sites, access glycoengineering tools (NetOGlyc, GlycoShield). Therapeutic antibody optimization and vaccine design.
adaptyvCloud laboratory platform for automated protein testing: binding assays, expression testing, thermostability, enzyme activity. Protein sequence optimization with NetSolP, SoluProt, ESM.
ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab for autonomous lab execution. Cell-free protein expression, protocol workflows, and biotech automation.

🧬 Bioinformatics (gptomics bio-* suite)

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Bioinformatics Tools & Pipelines

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SkillDescription
biopythonPrimary Python toolkit for molecular biology: PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), BLAST workflows.
scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, for microbiome analysis.
etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
nextflow-developmentRun nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use for RNA-seq, WGS/WES, or ATAC-seq from local FASTQs or public datasets (GEO/SRA).
fastq-analysisSRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines for bulk and single-cell sequencing data.
genimlGenomic interval data (BED files) for machine learning tasks. Train region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis.
gtarsHigh-performance genomic interval analysis in Rust with Python bindings. Genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models.
arboretoInfer gene regulatory networks (GRNs) from gene expression data using GRNBoost2 and GENIE3 algorithms. For bulk RNA-seq and single-cell RNA-seq regulatory network inference.
lamindbOpen-source biological data framework for queryable, traceable, reproducible, and FAIR datasets (scRNA-seq, genomics, imaging).
dnanexus-integrationDNAnexus cloud genomics platform. Build apps/applets, manage data, dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development.
latchbio-integrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, Nextflow/Snakemake integration.

Bioinformatics — Clinical Databases & Variant Analysis

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SkillDescription
bio-clinical-databases-clinvar-lookupQuery ClinVar for clinical variant classifications, pathogenicity assertions, and review status.
bio-clinical-databases-dbsnp-queriesQuery dbSNP for SNP frequency, allele, and functional annotation data.
bio-clinical-databases-gnomad-frequenciesRetrieve population allele frequencies from gnomAD for rare variant interpretation.
bio-clinical-databases-hla-typingHLA typing from sequencing data using standard typing tools and databases.
bio-clinical-databases-myvariant-queriesBatch query MyVariant.info for aggregated variant annotations from multiple databases.
bio-clinical-databases-pharmacogenomicsPharmGKB/CPIC pharmacogenomics variant lookup for drug-gene interactions.
bio-clinical-databases-polygenic-riskCalculate polygenic risk scores from GWAS summary statistics and genotype data.
bio-clinical-databases-somatic-signaturesExtract and classify mutational signatures from somatic variant catalogs (COSMIC).
bio-clinical-databases-tumor-mutational-burdenCompute tumor mutational burden (TMB) from somatic variant calls.
bio-clinical-databases-variant-prioritizationRank and filter candidate variants by pathogenicity scores, inheritance, and phenotype match.
bio-variant-callingGATK-based germline variant calling pipeline from aligned BAM/CRAM files.
bio-variant-calling-clinical-interpretationInterpret variant calls in clinical context with ACMG guidelines.
bio-variant-calling-deepvariantDeepVariant deep-learning variant caller for short-read WGS/WES data.
bio-variant-calling-filtering-best-practicesApply VQSR and hard-filtering best practices to variant call sets.
bio-variant-calling-joint-callingJoint genotyping across multiple samples for improved variant discovery.
bio-variant-calling-structural-variant-callingCall structural variants (SVs) from long-read or paired-end sequencing.
bio-variant-annotationAnnotate VCF files with functional, population, and clinical consequence data.
bio-variant-normalizationNormalize variant representations (left-alignment, decomposition) for consistent comparison.
bio-vcf-basicsRead, write, and parse VCF files; filter by quality, region, and sample.
bio-vcf-manipulationAdvanced VCF manipulation: merging, splitting, reformatting, subset extraction.
bio-vcf-statisticsCompute variant statistics: ts/tv ratio, heterozygosity, depth distributions.
bio-gatk-variant-callingEnd-to-end GATK HaplotypeCaller variant calling with BQSR and joint genotyping.
bio-copy-number-cnv-annotationAnnotate CNV calls with gene content, database overlap, and clinical significance.
bio-copy-number-cnv-visualizationVisualize copy number profiles and segment plots from WGS/WES data.
bio-copy-number-cnvkit-analysisCNVKit copy number analysis for targeted sequencing and WES data.
bio-copy-number-gatk-cnvGATK4 somatic copy number alteration calling pipeline.
bio-tumor-fraction-estimationEstimate tumor purity and ploidy from allele frequencies and copy number data.
bio-ctdna-mutation-detectionDetect circulating tumor DNA mutations from liquid biopsy ultra-deep sequencing.
bio-cfdna-preprocessingProcess cell-free DNA sequencing data: adapter trimming, deduplication, QC.
bio-methylation-based-detectionDetect methylation-based cancer signals from cfDNA methylation data.
bio-longitudinal-monitoringTrack somatic variant evolution and clonal dynamics across serial samples.

Bioinformatics — Sequencing & Read QC

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SkillDescription
bio-fastq-qualityAssess FASTQ read quality with FastQC/MultiQC; generate per-sample QC reports.
bio-read-qc-adapter-trimmingTrim sequencing adapters with Trimmomatic, Cutadapt, or fastp.
bio-read-qc-contamination-screeningScreen reads for human/microbial contamination using FastQ Screen or Kraken.
bio-read-qc-fastp-workflowEnd-to-end read QC and preprocessing with fastp including UMI handling.
bio-read-qc-quality-filteringApply quality-score and length filters to remove low-quality reads.
bio-read-qc-quality-reportsAggregate multi-sample QC reports with MultiQC.
bio-read-qc-umi-processingDeduplicate PCR duplicates using UMI-tools for accurate quantification.
bio-paired-end-fastqHandle paired-end FASTQ files: validation, interleaving, splitting.
bio-alignment-ioRead/write SAM/BAM/CRAM alignment files with pysam and samtools.
bio-alignment-msa-parsingParse and analyze multiple sequence alignments (FASTA, ClustalW, Stockholm).
bio-alignment-msa-statisticsCompute MSA statistics: conservation, gap content, entropy.
bio-alignment-pairwisePairwise sequence alignment using Smith-Waterman, Needleman-Wunsch, BLAST.
bio-longread-alignmentAlign long reads (ONT/PacBio) with minimap2; sort and index BAM files.
bio-longread-qcQuality control for long-read sequencing: read length, N50, error rate.
bio-longread-medakaConsensus polishing and variant calling with Oxford Nanopore Medaka.
bio-longread-structural-variantsCall large structural variants from long-read data with Sniffles/PBSV.
bio-basecallingBase-call raw ONT signals with Dorado/Guppy; convert FAST5 to FASTQ.
bio-compressed-filesHandle compressed bioinformatics files: bgzip, tabix, zstd, htslib.
bio-format-conversionConvert between bioinformatics formats: FASTQ↔FASTA, BAM↔CRAM, BED↔GTF.
bio-sequence-statisticsCompute sequence statistics: GC content, length distributions, complexity.
bio-read-sequencesRead and iterate over biological sequences from FASTA/FASTQ files.
bio-write-sequencesWrite biological sequences to FASTA/FASTQ with metadata preservation.
bio-filter-sequencesFilter sequences by length, quality, pattern, or taxonomy label.
bio-batch-processingBatch-process large bioinformatics datasets across samples and cohorts.
bio-rnaseq-qcRNA-seq specific QC: strandedness, rRNA contamination, gene body coverage.
bio-long-read-sequencing-clair3-variantsCall variants from long-read sequencing with Clair3 deep-learning model.
bio-long-read-sequencing-isoseq-analysisIso-Seq full-length transcript analysis for isoform discovery.
bio-long-read-sequencing-nanopore-methylationCall CpG methylation from Oxford Nanopore sequencing with Modbam2bed.
bio-splicing-qcRNA splicing quality assessment: junction read coverage, novel splice sites.
bio-splicing-quantificationQuantify alternative splicing events: PSI/inclusion levels per isoform.
bio-sashimi-plotsGenerate sashimi plots for visualizing RNA-seq splicing at specific loci.
bio-consensus-sequencesGenerate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus; useful for sample-specific references and haplotype reconstruction.

Bioinformatics — Differential Expression & Transcriptomics

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SkillDescription
bio-de-deseq2-basicsDESeq2 differential expression analysis: design matrix, size factors, dispersion.
bio-de-edger-basicsEdgeR differential expression for count data with empirical Bayes dispersion.
bio-de-resultsExtract, filter, and annotate DESeq2/EdgeR results tables.
bio-de-visualizationVolcano plots, MA plots, and heatmaps for differential expression results.
bio-differential-expression-batch-correctionRemove batch effects with ComBat/limma for multi-cohort DE analysis.
bio-differential-expression-timeseries-deTime-series differential expression with splines and mixed models.
bio-differential-splicingDetect differential alternative splicing events with rMATS or MAJIQ.
bio-isoform-switchingIdentify isoform switching events with DRIMSeq and IsoformSwitchAnalyzeR.
bio-ribo-seq-orf-detectionDetect translated ORFs from ribosome profiling data with RiboTaper/Ribo-TISH.
bio-ribo-seq-riboseq-preprocessingPreprocess ribosome profiling reads: adapter trimming, rRNA removal, alignment.
bio-ribo-seq-ribosome-periodicityAssess triplet periodicity and ribosome footprint quality in Ribo-seq data.
bio-ribo-seq-ribosome-stallingIdentify ribosome stalling sites and pausing from Ribo-seq profiles.
bio-ribo-seq-translation-efficiencyCompute translation efficiency ratios from matched RNA-seq and Ribo-seq.

Bioinformatics — Pathway & Network Analysis

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SkillDescription
bio-pathway-go-enrichmentGene Ontology enrichment analysis with clusterProfiler or g:Profiler.
bio-pathway-gseaGene Set Enrichment Analysis (GSEA) with pre-ranked or count-based statistics.
bio-pathway-kegg-pathwaysKEGG pathway enrichment and visualization for metabolic/signaling pathways.
bio-pathway-reactomeReactome pathway analysis with hierarchical enrichment and visualization.
bio-pathway-wikipathwaysWikiPathways enrichment and network visualization.
bio-pathway-enrichment-visualizationDot plots, enrichment maps, and network visualizations for pathway results.

Bioinformatics — Single-Cell & Spatial Omics

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SkillDescription
bio-single-cell-batch-integrationIntegrate scRNA-seq datasets across batches with Harmony, BBKNN, scVI.
bio-single-cell-cell-annotationAnnotate single-cell clusters using marker genes and reference atlases.
bio-single-cell-cell-communicationInfer ligand-receptor cell-cell communication with CellChat or NicheNet.
bio-single-cell-clusteringCluster single cells with Leiden/Louvain algorithms in Scanpy/Seurat.
bio-single-cell-data-ioRead/write AnnData, Seurat, and 10x Genomics h5ad/h5 formats.
bio-single-cell-doublet-detectionRemove doublets from scRNA-seq with Scrublet or DoubletFinder.
bio-single-cell-lineage-tracingReconstruct cell lineage trees from scRNA-seq with clonal barcodes.
bio-single-cell-markers-annotationIdentify cluster marker genes and auto-annotate cell types.
bio-single-cell-metabolite-communicationInfer metabolite-mediated intercellular communication from scRNA-seq.
bio-single-cell-multimodal-integrationIntegrate scRNA-seq with ATAC, CITE-seq, or spatial using WNN/MultiVI.
bio-single-cell-perturb-seqAnalyze genetic perturbation screens from Perturb-seq / CROP-seq data.
bio-single-cell-preprocessingSingle-cell preprocessing: count filtering, normalization, HVG selection.
bio-single-cell-scatac-analysisscATAC-seq peak calling, TF motif enrichment, and chromatin accessibility.
bio-single-cell-splicingRNA velocity and splicing dynamics with scVelo or Alevin.
bio-single-cell-trajectory-inferenceInfer pseudotime trajectories with Monocle3, PAGA, or Slingshot.
bio-spatial-transcriptomics-image-analysisAnalyze histology images co-registered with spatial transcriptomics data.
bio-spatial-transcriptomics-spatial-communicationLigand-receptor communication analysis with spatial context (COMMOT, SpatialDE).
bio-spatial-transcriptomics-spatial-data-ioLoad and process Visium, Slide-seq, MERFISH, and STARmap datasets.
bio-spatial-transcriptomics-spatial-deconvolutionDeconvolve cell type proportions in spatial spots with RCTD, SPOTlight.
bio-spatial-transcriptomics-spatial-domainsIdentify spatially variable genes and tissue domains with SpatialDE/BANKSY.
bio-spatial-transcriptomics-spatial-multiomicsIntegrate spatial transcriptomics with proteomics, metabolomics, or imaging.
bio-spatial-transcriptomics-spatial-neighborsBuild spatial neighbor graphs and perform neighborhood enrichment analysis.
bio-spatial-transcriptomics-spatial-preprocessingPreprocess spatial transcriptomics: QC, normalization, spot filtering.
bio-spatial-transcriptomics-spatial-proteomicsAnalyze spatial proteomics data from CODEX, IMC, or MIBI platforms.
bio-spatial-transcriptomics-spatial-statisticsSpatial statistics: Moran's I, spatial autocorrelation, co-localization.
bio-spatial-transcriptomics-spatial-visualizationVisualize spatial gene expression maps and tissue section overlays.

Bioinformatics — Epigenomics & Chromatin

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SkillDescription
bio-atac-seq-atac-peak-callingCall ATAC-seq chromatin accessibility peaks with MACS2/MACS3.
bio-atac-seq-atac-qcATAC-seq quality control: TSS enrichment, fragment size, FRiP score.
bio-atac-seq-differential-accessibilityDifferential chromatin accessibility between conditions with DESeq2/DiffBind.
bio-atac-seq-footprintingTranscription factor footprinting from ATAC-seq with TOBIAS or HINT-ATAC.
bio-atac-seq-motif-deviationTF motif deviation scoring with chromVAR for single-cell ATAC data.
bio-atac-seq-nucleosome-positioningInfer nucleosome positioning from ATAC-seq fragment length distributions.
bio-chipseq-differential-bindingDifferential ChIP-seq binding analysis with DiffBind.
bio-chipseq-motif-analysisDe novo and known motif discovery from ChIP-seq peaks with HOMER/MEME.
bio-chipseq-peak-annotationAnnotate ChIP-seq peaks with genomic features and nearest genes.
bio-chipseq-peak-callingCall ChIP-seq peaks with MACS2 for TF binding and histone marks.
bio-chipseq-qcChIP-seq quality metrics: FRiP, SCC, phantompeakqualtools.
bio-chipseq-super-enhancersIdentify super enhancers from H3K27ac ChIP-seq with ROSE.
bio-chipseq-visualizationHeatmaps and aggregate profiles at peak regions with deepTools.
bio-hi-c-analysis-compartment-analysisCall A/B compartments from Hi-C contact matrices.
bio-hi-c-analysis-contact-pairsProcess Hi-C contact pairs: filtering, deduplication, binning.
bio-hi-c-analysis-hic-data-ioRead and write Hi-C data formats: .hic, cool, mcool with cooler/hicstuff.
bio-hi-c-analysis-hic-differentialDifferential Hi-C interaction analysis between conditions.
bio-hi-c-analysis-hic-visualizationVisualize Hi-C contact maps, TADs, and loops with pyGenomeTracks.
bio-hi-c-analysis-loop-callingDetect chromatin loops from Hi-C data with Mustache or HICCUPS.
bio-hi-c-analysis-matrix-operationsNormalize Hi-C matrices: ICE, KR, VC; compute observed/expected.
bio-hi-c-analysis-tad-detectionIdentify topologically associating domains (TADs) from Hi-C data.
bio-methylation-bismark-alignmentAlign bisulfite sequencing reads and extract CpG methylation with Bismark.
bio-methylation-callingCall CpG methylation from WGBS/RRBS alignments.
bio-methylation-dmr-detectionIdentify differentially methylated regions (DMRs) with DSS or MethylKit.
bio-methylation-methylkitMethylation analysis with MethylKit: CpG tiles, DMR calling, annotation.

Bioinformatics — Metagenomics & Microbiome

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SkillDescription
bio-metagenomics-abundanceEstimate microbial taxon abundances from shotgun metagenomics.
bio-metagenomics-amr-detectionDetect antimicrobial resistance genes with AMRFinder or RGI/CARD.
bio-metagenomics-functional-profilingFunctional profiling of metagenomes with HUMAnN3 for pathway/gene families.
bio-metagenomics-krakenTaxonomic classification of metagenomic reads with Kraken2/Bracken.
bio-metagenomics-metaphlanClade-specific marker-based profiling of microbial communities with MetaPhlAn4.
bio-metagenomics-strain-trackingTrack microbial strains across samples with StrainPhlan or inStrain.
bio-metagenomics-visualizationVisualize microbiome composition with Krona charts and stacked bar plots.
bio-microbiome-amplicon-processingProcess 16S/ITS amplicon sequencing with QIIME2 or DADA2.
bio-microbiome-differential-abundanceTest differential microbial abundance with ANCOM-BC, MaAsLin2, or ALDEx2.
bio-microbiome-diversity-analysisAlpha/beta diversity analysis: Shannon, PD, UniFrac, PCoA.
bio-microbiome-functional-predictionPredict functional capacity from 16S data with PICRUSt2 or Tax4Fun.
bio-microbiome-qiime2-workflowEnd-to-end QIIME2 workflow: denoising, diversity, differential abundance.
bio-microbiome-taxonomy-assignmentAssign taxonomy to ASVs/OTUs using SILVA, GTDB, or Greengenes2.

Bioinformatics — Immunoinformatics & Flow Cytometry

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SkillDescription
bio-immunoinformatics-epitope-predictionPredict MHC-I/II epitopes from protein sequences with NetMHCpan/MHCflurry.
bio-immunoinformatics-immunogenicity-scoringScore peptide immunogenicity for vaccine and neoantigen prioritization.
bio-immunoinformatics-mhc-binding-predictionPredict peptide-MHC binding affinities for multiple alleles.
bio-immunoinformatics-neoantigen-predictionPredict neoantigens from somatic mutations for personalized cancer vaccines.
bio-immunoinformatics-tcr-epitope-bindingPredict TCR-epitope binding with ERGO, pMTnet, or NetTCR.
bio-tcr-bcr-analysis-immcantation-analysisAnalyze B/T cell receptor repertoires with the Immcantation suite.
bio-tcr-bcr-analysis-mixcr-analysisMiXCR V(D)J alignment and clonotype assembly for immune repertoires.
bio-tcr-bcr-analysis-repertoire-visualizationVisualize repertoire diversity, clonal expansion, and V-gene usage.
bio-tcr-bcr-analysis-scirpy-analysisSingle-cell TCR/BCR analysis integrated with scRNA-seq using Scirpy.
bio-tcr-bcr-analysis-vdjtools-analysisImmune repertoire statistics and overlap analysis with VDJtools.
bio-flow-cytometry-bead-normalizationNormalize flow cytometry data using calibration beads.
bio-flow-cytometry-clustering-phenotypingCluster and phenotype cell populations with FlowSOM, PhenoGraph, or UMAP.
bio-flow-cytometry-compensation-transformationApply compensation matrices and biexponential/arcsinh transformations.
bio-flow-cytometry-cytometry-qcQuality control for flow/mass cytometry: signal drift, spillover, outlier detection.
bio-flow-cytometry-differential-analysisStatistical comparison of cell populations between conditions.
bio-flow-cytometry-doublet-detectionDetect and remove doublets from flow cytometry data.
bio-flow-cytometry-fcs-handlingRead, write, and manipulate FCS files with FlowCore/FlowKit.
bio-flow-cytometry-gating-analysisManual and algorithmic gating strategies for cell population identification.
bio-imaging-mass-cytometry-cell-segmentationSegment cells in IMC images with Mesmer or CellProfiler.
bio-imaging-mass-cytometry-data-preprocessingPreprocess imaging mass cytometry data: hot pixel removal, normalization.
bio-imaging-mass-cytometry-interactive-annotationInteractively annotate cell types in IMC spatial datasets.
bio-imaging-mass-cytometry-phenotypingPhenotype immune and tumor cells from multi-marker IMC panels.
bio-imaging-mass-cytometry-quality-metricsQuality metrics for IMC acquisitions: signal-to-noise, tissue coverage.
bio-imaging-mass-cytometry-spatial-analysisSpatial cell neighborhood analysis from imaging mass cytometry data.

Bioinformatics — Multi-Omics Integration

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SkillDescription
bio-multi-omics-data-harmonizationHarmonize multi-omics datasets: sample matching, batch correction, feature alignment.
bio-multi-omics-mixomics-analysisMulti-omics factor analysis with mixOmics (DIABLO, MOFA, sPLS-DA).
bio-multi-omics-mofa-integrationMulti-Omics Factor Analysis (MOFA+) for latent factor discovery across modalities.
bio-multi-omics-similarity-networkSimilarity Network Fusion (SNF) for patient stratification from multi-omics.

Bioinformatics — Proteomics & Metabolomics

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SkillDescription
bio-proteomics-data-importImport DDA/DIA proteomics data from MaxQuant, Proteome Discoverer, FragPipe.
bio-proteomics-dia-analysisDIA proteomics analysis with DIA-NN or Spectronaut.
bio-proteomics-differential-abundanceDifferential protein abundance with limma, MSstats, or DEqMS.
bio-proteomics-peptide-identificationPeptide spectrum matching and database search result parsing.
bio-proteomics-protein-inferenceProtein grouping, parsimony, and FDR control for proteomics experiments.
bio-proteomics-proteomics-qcProteomics QC: peptide counts, coverage, missing values, CV.
bio-proteomics-ptm-analysisPost-translational modification analysis: phospho, ubiquitin, glycan enrichment.
bio-proteomics-quantificationLabel-free, TMT/iTRAQ, and SILAC quantification workflows.
bio-proteomics-spectral-librariesBuild and use spectral libraries for DIA data analysis.
bio-metabolomics-lipidomicsLipidomics data analysis: lipid class annotation, fatty acid composition.
bio-metabolomics-metabolite-annotationAnnotate mass spec features with HMDB, MZmine, SIRIUS, or MetFrag.
bio-metabolomics-msdial-preprocessingMS-DIAL-based LC-MS/GC-MS data preprocessing and peak detection.
bio-metabolomics-normalization-qcMetabolomics normalization: PQN, LOESS, median, batch correction.
bio-metabolomics-pathway-mappingMap identified metabolites to KEGG, MetaCyc, or Reactome pathways.
bio-metabolomics-statistical-analysisUnivariate/multivariate stats for metabolomics: PCA, PLS-DA, ANOVA.
bio-metabolomics-targeted-analysisTargeted metabolomics with MRM/SRM: calibration curves, quantification.
bio-metabolomics-xcms-preprocessingXCMS-based LC-MS peak detection, alignment, and grouping.

Bioinformatics — Structural Biology & Cheminformatics

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SkillDescription
bio-structural-biology-alphafold-predictionsUse AlphaFold2/3 predictions: model quality assessment, confidence scores.
bio-structural-biology-modern-structure-predictionModern structure prediction with ESMFold, RoseTTAFold, and OpenFold.
bio-pdb-geometric-analysisGeometric analysis of protein structures: distances, angles, contacts, RMSD.
bio-pdb-structure-ioRead and write PDB/mmCIF structure files with BioPython or Gemmi.
bio-pdb-structure-modificationModify protein structures: add hydrogens, mutate residues, energy minimize.
bio-pdb-structure-navigationNavigate and inspect PDB structures: chain, residue, atom selection.
bio-molecular-descriptorsCalculate molecular descriptors (RDKit): MW, LogP, TPSA, fingerprints.
bio-molecular-ioRead/write chemical structure formats: SDF, SMILES, MOL2, PDB with RDKit.
bio-reaction-enumerationEnumerate reactions and products from SMARTS reaction templates.
bio-similarity-searchingMolecular similarity search: Tanimoto, fingerprint-based, scaffold hopping.
bio-substructure-searchSubstructure searching in chemical databases using SMARTS patterns.
bio-virtual-screeningVirtual screening workflows: docking, scoring, pose filtering with AutoDock/Vina.
bio-admet-predictionPredict ADMET properties: absorption, distribution, metabolism, excretion, toxicity.

Bioinformatics — Epidemiological & Causal Genomics

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SkillDescription
bio-epidemiological-genomics-amr-surveillanceAntimicrobial resistance surveillance from genomic epidemiology data.
bio-epidemiological-genomics-pathogen-typingPathogen molecular typing: MLST, wgMLST, cgMLST for outbreak analysis.
bio-epidemiological-genomics-phylodynamicsPhylodynamics: molecular clock, population dynamics, BEAST2/TreeTime.
bio-epidemiological-genomics-transmission-inferenceInfer transmission networks from pathogen genomics with TransPhylo/outbreaker2.
bio-epidemiological-genomics-variant-surveillanceTrack pathogen variant emergence and spread from genomic surveillance.
bio-causal-genomics-colocalization-analysisColocalization analysis of GWAS and eQTL signals with coloc or eCAVIAR.
bio-causal-genomics-fine-mappingFine-map causal variants at GWAS loci with SuSiE or FINEMAP.
bio-causal-genomics-mediation-analysisCausal mediation analysis for gene expression intermediaries.
bio-causal-genomics-mendelian-randomizationTwo-sample Mendelian randomization with MR-Base/TwoSampleMR.
bio-causal-genomics-pleiotropy-detectionDetect horizontal pleiotropy and heterogeneity in MR analyses.
bio-genome-engineering-base-editing-designDesign base editors (CBE/ABE) for precise single-base correction.
bio-genome-engineering-grna-designDesign and score CRISPR guide RNAs with Cas-OFFinder and CRISPOR.
bio-genome-engineering-hdr-template-designDesign HDR templates for precise knock-in via homology-directed repair.
bio-genome-engineering-off-target-predictionPredict CRISPR off-target sites genome-wide for safety assessment.
bio-genome-engineering-prime-editing-designDesign pegRNAs and nickase gRNAs for prime editing experiments.
bio-crispr-screens-base-editing-analysisAnalyze base editing screens: guide efficiency, editing outcomes.
bio-crispr-screens-batch-correctionCorrect batch effects in CRISPR screen data across replicates.
bio-crispr-screens-crispresso-editingQuantify editing outcomes with CRISPResso2 from amplicon sequencing.
bio-crispr-screens-hit-callingCall hits from CRISPR screens using MAGeCK, BAGEL2, or casTLE.
bio-crispr-screens-jacks-analysisCRISPR screen analysis with JACKS hierarchical Bayesian model.
bio-crispr-screens-library-designDesign CRISPR screen libraries: guide selection, controls, coverage.
bio-crispr-screens-mageck-analysisMAGeCK MLE/RRA analysis for CRISPR pooled screens.
bio-crispr-screens-screen-qcQuality control for CRISPR screens: Gini index, read distribution.

🔬 Omics & Computational Biology

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Single-Cell & Spatial Omics

Click to expand skill list
SkillDescription
anndataWorking with annotated data matrices in Python for single-cell genomics analysis, managing experimental measurements with metadata and large-scale omics data.
scanpySingle-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory.
scvi-toolsDeep learning for single-cell analysis: data integration/batch correction (scVI/scANVI), ATAC-seq (PeakVI), CITE-seq (totalVI), multiome (MultiVI), spatial deconvolution (DestVI).
single-cell-rna-qcQuality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
cellxgene-censusQuery CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots.
bulk-combat-correctionRemove batch effects from merged bulk RNA-seq or microarray cohorts using pyComBat, with corrected matrix export and pre/post correction visualizations.
bulk-deg-analysisBulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, visualization, and pathway enrichment via OmicVerse.
bulk-deseq2-analysisPyDESeq2-based differential expression analysis with ID mapping, DE testing, fold-change thresholding, and enrichment visualization.
bulk-stringdb-ppiQuery STRING for protein interactions, build PPI graphs with pyPPI, and render network figures for bulk gene lists.
bulk-to-single-deconvolutionConvert bulk RNA-seq cohorts to synthetic single-cell datasets using Bulk2Single workflow for cell fraction estimation and beta-VAE generation.
bulk-trajblend-interpolationExtend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq using beta-VAE and GNN models.
bulk-wgcna-analysisRun PyWGCNA through OmicVerse — co-expression module construction, eigengene visualization, and hub gene extraction.
single-annotationSingle-cell annotation workflows: SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer for annotating cell types across modalities.
single-cellphone-dbRun CellPhoneDB v5 on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualizations.
single-clusteringSingle-cell clustering workflow: QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration in OmicVerse.
single-downstream-analysisOmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports for single-cell data.
single-multiomicsOmicVerse multi-omics tutorials: MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
single-preprocessingSingle-cell preprocessing in OmicVerse: QC, normalization, HVG detection, PCA/embedding pipelines (CPU/GPU).
single-to-spatial-mappingMap scRNA-seq atlases onto spatial transcriptomics slides using Single2Spatial workflow for deep-forest training and marker visualization.
single-trajectoryOmicVerse trajectory workflows: PAGA, Palantir, VIA, velocity coupling, and fate scoring.
spatial-tutorialsSpatial transcriptomics tutorials: preprocessing, deconvolution, and downstream modeling across Visium, Visium HD, Stereo-seq, and Slide-seq.
tcga-preprocessingIngest TCGA sample sheets, expression archives, and clinical carts into OmicVerse, with survival metadata initialization and AnnData export.
gsea-enrichmentGene set enrichment analysis in OmicVerse with correct geneset format handling for loading pathway databases and running GSEA.

Cheminformatics & Drug Discovery

Click to expand skill list
SkillDescription
rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity.
datamolPythonic RDKit wrapper with simplified interface for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformer generation.
medchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
diffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
molfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
deepchemMolecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, for drug discovery ML.
torchdrugGraph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs.
torch_geometricGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, molecular property prediction, for geometric

常见问题

What is OpenClaw-Medical-Skills?

OpenClaw-Medical-Skills is an open-source ai agents skill for AI coding assistants such as Claude Code, Codex CLI, and ChatGPT, built by FreedomIntelligence. The largest open-source medical AI skills library for OpenClaw🦞. It has 2,964 GitHub stars.

Is OpenClaw-Medical-Skills safe to use?

OpenClaw-Medical-Skills returned warnings in SkillsLLM's automated security scan. It has no critical vulnerabilities, but review the flagged issues in the Security Report section before adding it to your workflow.

How do I install OpenClaw-Medical-Skills?

Clone the repository with "git clone https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills" and add it to your Claude Code skills directory (see the Installation section above).

What programming language is OpenClaw-Medical-Skills written in?

OpenClaw-Medical-Skills is primarily written in Python. It is open-source under FreedomIntelligence on GitHub, so you can review or fork the full source.

Are there alternatives to OpenClaw-Medical-Skills?

Yes. SkillsLLM lists many other AI Agents skills you can browse and compare side by side. Open the AI Agents category from the badge at the top of this page, or use the Related Skills and comparison links further down to weigh OpenClaw-Medical-Skills against similar tools.

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