OpenClaw Medical Skills

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

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

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 Skills	With OpenClaw Medical Skills
Generic AI responses about medicine	Real PubMed / ClinicalTrials.gov / FDA queries
No bioinformatics capability	RNA-seq, scRNA-seq, GWAS, variant calling pipelines
No drug intelligence	ChEMBL, DrugBank, DDI prediction, pharmacovigilance
No clinical documentation	SOAP notes, discharge summaries, prior auth decisions
No genomics support	VCF annotation, ACMG classification, PRS calculation
No regulatory guidance	FDA, 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:

Priority	Path	Scope
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

Category	Count	Highlights
General & Core	10	Browser/search, document tools, and developer workflow utilities
Medical & Clinical	119	Clinical reports, CDS, oncology, imaging, and healthcare AI
Scientific Databases	43	Genomics/protein/drug databases and biomedical knowledge retrieval
Bioinformatics (gptomics)	239	Variant analysis, sequencing QC, DE, pathways, single-cell, and epigenomics
Omics & Computational Biology	59	Single-cell/spatial, proteomics, cheminformatics, and protein design tools
ClawBio Pipelines	21	Orchestration pipelines for scRNA, GWAS, ancestry, and structural workflows
BioOS Extended Suite	285	Extended agent suite for oncology, immunology, clinical AI, and infrastructure
Data Science & Tools	93	Statistics, visualization, automation, simulation, and scientific tooling
Total	869

General & Core

General Tools

Medical & Clinical

Scientific Databases

Bioinformatics (gptomics bio-* suite)

Omics & Computational Biology

ClawBio Pipelines

BioOS Extended Suite

Data Science & Tools

Skills List

🧰 General & Core

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General Tools

Click to expand skill list

Skill	Description
agent-browser	Browse 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-skills	Helps 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-engine	Multi 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-search	Search and fetch structured content from Wikipedia using the MediaWiki API for reliable, encyclopedic information. Supports multi-language queries.
deep-research	Execute 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.
pdf	Comprehensive PDF toolkit — extract text and tables, create new PDFs, merge/split documents, handle forms, OCR scanned PDFs. Use when working with any .pdf file.
docx	Create, 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.
xlsx	Spreadsheet creation, editing, and analysis. Supports formulas, formatting, data analysis, and visualization. Use for any .xlsx, .xlsm, .csv, or .tsv task.
pptx	Presentation creation, editing, and analysis. Supports layouts, speaker notes, templates, and design. Use for any .pptx file.
doc-coauthoring	Guide users through a structured workflow for co-authoring documentation. Use when writing documentation, proposals, technical specs, decision docs, or similar structured content.

🏥 Medical & Clinical

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Medical Tools

Click to expand skill list

Skill	Description
pubmed-search	Search 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-toolkit	Query 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-briefs	Generate 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.).
usmle	Prepare 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-extractor	Extract medical entities (symptoms, medications, lab values, diagnoses) from patient messages.
patiently-ai	Simplifies medical documents for patients. Takes doctor's letters, test results, prescriptions, discharge summaries, and clinical notes and explains them in clear, personalised language.
biomedical-search	Complete biomedical information search combining PubMed, preprints, clinical trials, and FDA drug labels. Powered by Valyu semantic search.
medical-imaging-review	Write comprehensive literature reviews for medical imaging AI research. Use when writing survey papers, systematic reviews, or literature analyses on imaging topics.
fhir-developer-skill	FHIR API development guide for building healthcare endpoints (Patient, Observation, Encounter, Condition, MedicationRequest). Use when developing or integrating FHIR REST APIs.
clinical-trial-protocol-skill	Generate 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-skill	Automate payer review of prior authorization (PA) requests. Assesses medical necessity, validates against coverage policies, and generates PA decisions.
clinical-reports	Write 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-database	Query 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-support	Generate 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-design	Strategic 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-research	Generate 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-research	Deep 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-guidelines	Search 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-research	Comprehensive 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-repurposing	Identify 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-interaction	Drug-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-diagnosis	Differential 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-pharmacovigilance	Analyze 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-matching	Patient-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-review	Systematic literature reviews across multiple databases (PubMed, arXiv, bioRxiv, Semantic Scholar). Produces professionally formatted reports with verified citations in APA, Nature, Vancouver styles.
tooluniverse-precision-oncology	Actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, clinical trials, and resistance mechanisms.
tooluniverse-cancer-variant-interpretation	Clinical interpretation of somatic mutations in cancer. Given gene+variant (e.g., EGFR L858R, BRAF V600E), assesses oncogenicity, therapeutic implications, and trial eligibility.
tooluniverse-variant-analysis	Production-ready VCF processing, variant annotation, and mutation analysis. Parses VCF files, annotates with ClinVar/gnomAD/COSMIC, and interprets clinical significance.
tooluniverse-variant-interpretation	Systematic clinical variant interpretation from raw calls to ACMG-classified recommendations. Aggregates evidence from ClinVar, gnomAD, literature, and population databases.
tooluniverse-structural-variant-analysis	Comprehensive structural variant (SV/CNV) analysis for clinical genomics. Classifies SVs, assesses pathogenicity, and interprets copy number alterations.
tooluniverse-polygenic-risk-score	Build and interpret polygenic risk scores (PRS) for complex diseases using GWAS summary statistics. Calculates genetic risk profiles and interprets PRS percentiles.
tooluniverse-precision-medicine-stratification	Patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Identifies treatment-relevant subgroups and biomarker-driven therapy options.
tooluniverse-gwas-trait-to-gene	Discover genes associated with diseases and traits using GWAS Catalog (500k+ associations) and Open Targets Genetics locus-to-gene predictions.
tooluniverse-gwas-drug-discovery	Transform GWAS signals into drug targets and repurposing opportunities. Performs locus-to-gene mapping, druggability assessment, and existing drug identification.
tooluniverse-gwas-study-explorer	Compare GWAS studies and assess replication across cohorts. Integrates NHGRI-EBI GWAS Catalog and Open Targets Genetics for cross-study meta-analysis.
tooluniverse-gwas-finemapping	Identify and prioritize causal variants at GWAS loci using statistical fine-mapping. Computes posterior probabilities and credible sets for causal variant identification.
tooluniverse-gwas-snp-interpretation	Interpret SNPs from GWAS studies by aggregating evidence from GWAS Catalog, Open Targets Genetics, and ClinVar. Retrieves variant-trait associations and functional annotations.
tooluniverse-phylogenetics	Phylogenetics and sequence analysis — alignment processing, evolutionary tree construction, and evolutionary metrics for pathogens or species.
tooluniverse-epigenomics	Epigenomics data processing — methylation array analysis (CpG filtering, differential methylation), chromatin accessibility, and histone modification analysis.
tooluniverse-rnaseq-deseq2	RNA-seq differential expression analysis using PyDESeq2. Performs normalization, dispersion estimation, Wald testing, LFC shrinkage, and pathway enrichment.
tooluniverse-single-cell	Single-cell RNA-seq analysis using scanpy. Performs QC, normalization, PCA, UMAP, Leiden clustering, trajectory analysis, and cell type annotation.
tooluniverse-spatial-transcriptomics	Spatial transcriptomics data analysis — maps gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, and Slide-seq platforms.
tooluniverse-spatial-omics-analysis	Computational analysis for spatial multi-omics data integration — spatially variable genes, domain annotation, and tissue-resolved omics.
tooluniverse-proteomics-analysis	Mass spectrometry proteomics analysis — protein quantification, differential expression, PTMs, and protein-protein interaction network construction.
tooluniverse-metabolomics	Metabolomics research — identifies metabolites and searches databases (HMDB 220k+ metabolites, MetaboLights, Metabolomics Workbench).
tooluniverse-metabolomics-analysis	Metabolomics data analysis — metabolite identification, quantification, pathway analysis, and metabolic flux from LC-MS, GC-MS, or NMR data.
tooluniverse-multi-omics-integration	Integrate transcriptomics, proteomics, epigenomics, genomics, and metabolomics for systems biology and precision medicine.
tooluniverse-multiomic-disease-characterization	Systems-level disease characterization integrating genomics, transcriptomics, proteomics, pathway, and therapeutic layers.
tooluniverse-expression-data-retrieval	Retrieve gene expression and omics datasets from ArrayExpress and BioStudies with quality assessment and structured reports.
tooluniverse-gene-enrichment	Gene enrichment and pathway analysis using gseapy, PANTHER, STRING, Reactome. Supports GO enrichment, KEGG pathways, and 40+ ToolUniverse tools.
tooluniverse-systems-biology	Systems biology and pathway analysis using Reactome, KEGG, WikiPathways, Pathway Commons, and BioModels. Network modeling and pathway simulation.
tooluniverse-protein-interactions	Protein-protein interaction network analysis using STRING, BioGRID, and SASBDB. Maps interaction networks with confidence scores and functional modules.
tooluniverse-protein-structure-retrieval	Retrieve protein structure data from RCSB PDB, PDBe, and AlphaFold with quality assessment and comprehensive structural profiles.
tooluniverse-protein-therapeutic-design	Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design — RFdiffusion, ProteinMPNN, and ESM.
tooluniverse-antibody-engineering	Antibody engineering and optimization for therapeutics — humanization, affinity maturation, developability assessment, and immunogenicity prediction.
tooluniverse-immune-repertoire-analysis	TCR/BCR repertoire analysis from sequencing data — clonality, diversity, V(D)J gene usage, clonal expansion, and antigen specificity prediction.
tooluniverse-immunotherapy-response-prediction	Predict patient response to immune checkpoint inhibitors using multi-biomarker integration — TMB, MSI, PD-L1, TIL signatures, and HLA typing.
tooluniverse-infectious-disease	Pathogen characterization and drug repurposing for infectious disease outbreaks. Identifies taxonomy, essential proteins, structural targets, and treatment options.
tooluniverse-crispr-screen-analysis	CRISPR screen analysis for functional genomics — pooled or arrayed screens (knockout/activation/interference) to identify essential genes and hits.
tooluniverse-target-research	Comprehensive biological target intelligence — protein info, structure, interactions, pathways, expression, variant landscape, and drug pipeline.
tooluniverse-network-pharmacology	Compound-target-disease network analysis for drug repurposing, polypharmacology discovery, and systems pharmacology.
tooluniverse-statistical-modeling	Statistical modeling on biomedical datasets — linear/logistic regression, mixed-effects models, survival analysis, and Bayesian methods.
tooluniverse-image-analysis	Biomedical microscopy image analysis — colony morphometry, cell counting, fluorescence quantification, and statistical comparison of imaging data.
literature-search	Comprehensive scientific literature search across PubMed, arXiv, bioRxiv, medRxiv using natural language queries powered by Valyu semantic search.
medrxiv-search	Search medRxiv medical preprints with natural language queries powered by Valyu semantic search.
clinical-trials-search	Search ClinicalTrials.gov with natural language queries — find trials by condition, enrollment status, and outcomes via Valyu.
drug-discovery-search	End-to-end drug discovery platform combining ChEMBL, DrugBank, targets, and FDA labels via natural language Valyu search.
drug-labels-search	Search FDA drug labels with natural language queries — indications, dosing, and safety data via Valyu.
chembl-search	Search ChEMBL bioactive molecules database — compounds, assay data, and bioactivity via Valyu semantic search.
open-targets-search	Search Open Targets drug-disease associations and target validation via Valyu semantic search.
patents-search	Search global patents with natural language queries — prior art, patent landscapes, and innovation tracking via Valyu.
drugbank-search	Search DrugBank comprehensive drug database — mechanisms, interactions, and safety data via Valyu semantic search.
arxiv-search	Search arXiv preprints (biology, medicine, AI) using natural language queries powered by Valyu semantic search.
gwas-database	Query 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-survival	Survival 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

Skill	Description
tooluniverse-adverse-event-detection	Detect 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-discovery	Discover 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-retrieval	Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Comprehensive compound profiles with identifiers, properties, bioactivity.
tooluniverse-chemical-safety	Comprehensive 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-validation	Computational validation of drug targets across 10 dimensions: disambiguation, disease association, druggability, chemical matter, clinical precedent, safety, and expression evidence.
tooluniverse-sequence-retrieval	Retrieve biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles.

Medical Imaging & Pathology

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Skill	Description
pydicom	Python library for working with DICOM medical imaging files. Reading, writing, modifying DICOM data, extracting pixel data, handling metadata and multi-frame files.
histolab	Digital pathology image processing toolkit for whole slide images (WSI). Process H&E or IHC stained tissue images, extract tiles from gigapixel slides.
pathml	Computational pathology toolkit for analyzing WSI and multiparametric imaging data. H&E stained images, multiplex immunofluorescence, spatial omics integration.
omero-integration	Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, for high-content screening workflows.
neurokit2	Comprehensive biosignal processing: ECG, EEG, EDA, RSP, PPG, EMG, EOG signals. Cardiovascular signal analysis, neurophysiology, and physiological data processing.
neuropixels-analysis	Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, for neuroscience research.

Healthcare ML & Clinical AI

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Skill	Description
pyhealth	Comprehensive healthcare AI toolkit for developing ML models with clinical data (EHR, claims). Task definition API, model training, evaluation for clinical NLP and prediction.
scikit-learn	Machine learning in Python: supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning.
transformers	Pre-trained transformer models for NLP, computer vision, audio, and multimodal tasks. Text generation, classification, question answering, and biomedical NLP (BioBERT, ClinicalBERT).
shap	Model interpretability using SHAP (SHapley Additive exPlanations). Explain ML model predictions, compute feature importance, generate SHAP plots for biomedical models.
umap-learn	UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), for high-dimensional omics data.

Health & Wellness Analytics

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

Mental Health & Crisis Intervention

Click to expand skill list

Skill	Description
crisis-detection-intervention-ai	Detect 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-protocol	Handle mental health crisis situations safely: crisis detection, safety protocols, emergency escalation, suicide prevention, and hotline integration for AI coaching applications.
hipaa-compliance	Ensure HIPAA compliance when handling PHI. Audit logging, data access controls, security event tracking, and compliance verification for health data applications.
clinical-diagnostic-reasoning	Identify and counteract cognitive biases in medical decision-making through systematic error analysis, differential diagnosis frameworks, and clinical judgment improvement.
speech-pathology-ai	AI-powered speech-language pathology: phoneme analysis, articulation visualization, voice disorder assessment, fluency intervention, AAC, and stuttering treatment support.
hrv-alexithymia-expert	Heart rate variability biometrics and emotional awareness training. HRV analysis, interoception training, biofeedback, vagal tone assessment, and autonomic nervous system evaluation.
adhd-daily-planner	ADHD-optimized daily planning: time-blind friendly scheduling, executive function support, dopamine-aware task design, and neurodivergent-friendly productivity systems.
grief-companion	Compassionate bereavement support, memorial creation, grief education, and healing journey guidance through the non-linear path of loss.
jungian-psychologist	Jungian analytical psychology: shadow work, archetypal analysis, dream interpretation, active imagination, addiction/recovery through depth psychology lens, and individuation process.
modern-drug-rehab-computer	Comprehensive addiction recovery knowledge system: evidence-based treatment (CBT, DBT, MI, EMDR, MAT), recovery resources, crisis intervention, and family systems for rehab environments.
recovery-community-moderator	Trauma-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

Skill	Description
iso-13485-certification	Comprehensive 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

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Scientific Databases (Genomics & Variants)

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Skill	Description
clinvar-database	Query 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-database	Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
cosmic-database	Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
ensembl-database	Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
gene-database	Query 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-database	Access 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-database	Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines.
gget	CLI/Python toolkit for rapid bioinformatics queries with access to 20+ databases: Ensembl, UniProt, AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, BLAST, and more.
pysam	Genomic 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

Skill	Description
alphafold-database	Access 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-database	Access 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-database	Direct 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-database	Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
kegg-database	Direct REST API access to KEGG (academic use). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion.
reactome-database	Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology.
brenda-database	Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, substrate-specific enzyme info for biochemical research.
hmdb-database	Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics.
metabolomics-workbench-database	Access 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-database	Query PubChem via PUG-REST API (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
chembl-database	Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, for medicinal chemistry.
drugbank-database	Access comprehensive drug information from DrugBank including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data.
zinc-database	Access ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity searches, 3D-ready structures for docking, analog discovery, for virtual screening.
opentargets-database	Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
fda-database	Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis.
pubmed-database	Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management.
openalex-database	Query and analyze scholarly literature using the OpenAlex database. Search for academic papers, analyze research trends, find works by authors or institutions.
biorxiv-database	Search bioRxiv preprint server by keywords, authors, date ranges, or categories, retrieving paper metadata for life sciences preprint discovery.
bioservices	Primary Python tool for 40+ bioinformatics services. Unified API for UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO — preferred for multi-database workflows.
uspto-database	Access 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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Skill	Description
cbioportal-database	Query 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.
depmap	Query 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-commons	Query 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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Skill	Description
bindingdb-database	Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Drug discovery, lead optimization, polypharmacology, and SAR studies.
gnomad-database	Query gnomAD for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Variant pathogenicity interpretation and rare disease genetics.
gtex-database	Query GTEx for tissue-specific gene expression, eQTLs, and sQTLs. Link GWAS variants to gene regulation and interpret non-coding variant effects.
interpro-database	Query InterPro for protein family, domain, and functional site annotations. Integrates Pfam, PANTHER, PRINTS, SMART, and 11+ databases for protein function prediction.
jaspar-database	Query JASPAR for transcription factor binding site profiles (PWMs/PFMs). Regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.
monarch-database	Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations. Integrates OMIM, ORPHANET, HPO, ClinVar for rare disease gene discovery.
tiledbvcf	Scalable VCF/BCF ingestion, storage, and parallel queries using TileDB for population genomics at scale.

Structural Biology & Drug Discovery

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Skill	Description
molecular-dynamics	Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Protein/small molecule systems, force fields, energy minimization, RMSD/RMSF analysis, free energy surfaces.
glycoengineering	Analyze and engineer protein glycosylation. Predict N/O-glycosylation sites, access glycoengineering tools (NetOGlyc, GlycoShield). Therapeutic antibody optimization and vaccine design.
adaptyv	Cloud laboratory platform for automated protein testing: binding assays, expression testing, thermostability, enzyme activity. Protein sequence optimization with NetSolP, SoluProt, ESM.
ginkgo-cloud-lab	Submit 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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Skill	Description
biopython	Primary Python toolkit for molecular biology: PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), BLAST workflows.
scikit-bio	Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, for microbiome analysis.
etetoolkit	Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
deeptools	NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
nextflow-development	Run 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-analysis	SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines for bulk and single-cell sequencing data.
geniml	Genomic interval data (BED files) for machine learning tasks. Train region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis.
gtars	High-performance genomic interval analysis in Rust with Python bindings. Genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models.
arboreto	Infer 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.
lamindb	Open-source biological data framework for queryable, traceable, reproducible, and FAIR datasets (scRNA-seq, genomics, imaging).
dnanexus-integration	DNAnexus cloud genomics platform. Build apps/applets, manage data, dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development.
latchbio-integration	Latch 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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Skill	Description
bio-clinical-databases-clinvar-lookup	Query ClinVar for clinical variant classifications, pathogenicity assertions, and review status.
bio-clinical-databases-dbsnp-queries	Query dbSNP for SNP frequency, allele, and functional annotation data.
bio-clinical-databases-gnomad-frequencies	Retrieve population allele frequencies from gnomAD for rare variant interpretation.
bio-clinical-databases-hla-typing	HLA typing from sequencing data using standard typing tools and databases.
bio-clinical-databases-myvariant-queries	Batch query MyVariant.info for aggregated variant annotations from multiple databases.
bio-clinical-databases-pharmacogenomics	PharmGKB/CPIC pharmacogenomics variant lookup for drug-gene interactions.
bio-clinical-databases-polygenic-risk	Calculate polygenic risk scores from GWAS summary statistics and genotype data.
bio-clinical-databases-somatic-signatures	Extract and classify mutational signatures from somatic variant catalogs (COSMIC).
bio-clinical-databases-tumor-mutational-burden	Compute tumor mutational burden (TMB) from somatic variant calls.
bio-clinical-databases-variant-prioritization	Rank and filter candidate variants by pathogenicity scores, inheritance, and phenotype match.
bio-variant-calling	GATK-based germline variant calling pipeline from aligned BAM/CRAM files.
bio-variant-calling-clinical-interpretation	Interpret variant calls in clinical context with ACMG guidelines.
bio-variant-calling-deepvariant	DeepVariant deep-learning variant caller for short-read WGS/WES data.
bio-variant-calling-filtering-best-practices	Apply VQSR and hard-filtering best practices to variant call sets.
bio-variant-calling-joint-calling	Joint genotyping across multiple samples for improved variant discovery.
bio-variant-calling-structural-variant-calling	Call structural variants (SVs) from long-read or paired-end sequencing.
bio-variant-annotation	Annotate VCF files with functional, population, and clinical consequence data.
bio-variant-normalization	Normalize variant representations (left-alignment, decomposition) for consistent comparison.
bio-vcf-basics	Read, write, and parse VCF files; filter by quality, region, and sample.
bio-vcf-manipulation	Advanced VCF manipulation: merging, splitting, reformatting, subset extraction.
bio-vcf-statistics	Compute variant statistics: ts/tv ratio, heterozygosity, depth distributions.
bio-gatk-variant-calling	End-to-end GATK HaplotypeCaller variant calling with BQSR and joint genotyping.
bio-copy-number-cnv-annotation	Annotate CNV calls with gene content, database overlap, and clinical significance.
bio-copy-number-cnv-visualization	Visualize copy number profiles and segment plots from WGS/WES data.
bio-copy-number-cnvkit-analysis	CNVKit copy number analysis for targeted sequencing and WES data.
bio-copy-number-gatk-cnv	GATK4 somatic copy number alteration calling pipeline.
bio-tumor-fraction-estimation	Estimate tumor purity and ploidy from allele frequencies and copy number data.
bio-ctdna-mutation-detection	Detect circulating tumor DNA mutations from liquid biopsy ultra-deep sequencing.
bio-cfdna-preprocessing	Process cell-free DNA sequencing data: adapter trimming, deduplication, QC.
bio-methylation-based-detection	Detect methylation-based cancer signals from cfDNA methylation data.
bio-longitudinal-monitoring	Track somatic variant evolution and clonal dynamics across serial samples.

Bioinformatics — Sequencing & Read QC

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Skill	Description
bio-fastq-quality	Assess FASTQ read quality with FastQC/MultiQC; generate per-sample QC reports.
bio-read-qc-adapter-trimming	Trim sequencing adapters with Trimmomatic, Cutadapt, or fastp.
bio-read-qc-contamination-screening	Screen reads for human/microbial contamination using FastQ Screen or Kraken.
bio-read-qc-fastp-workflow	End-to-end read QC and preprocessing with fastp including UMI handling.
bio-read-qc-quality-filtering	Apply quality-score and length filters to remove low-quality reads.
bio-read-qc-quality-reports	Aggregate multi-sample QC reports with MultiQC.
bio-read-qc-umi-processing	Deduplicate PCR duplicates using UMI-tools for accurate quantification.
bio-paired-end-fastq	Handle paired-end FASTQ files: validation, interleaving, splitting.
bio-alignment-io	Read/write SAM/BAM/CRAM alignment files with pysam and samtools.
bio-alignment-msa-parsing	Parse and analyze multiple sequence alignments (FASTA, ClustalW, Stockholm).
bio-alignment-msa-statistics	Compute MSA statistics: conservation, gap content, entropy.
bio-alignment-pairwise	Pairwise sequence alignment using Smith-Waterman, Needleman-Wunsch, BLAST.
bio-longread-alignment	Align long reads (ONT/PacBio) with minimap2; sort and index BAM files.
bio-longread-qc	Quality control for long-read sequencing: read length, N50, error rate.
bio-longread-medaka	Consensus polishing and variant calling with Oxford Nanopore Medaka.
bio-longread-structural-variants	Call large structural variants from long-read data with Sniffles/PBSV.
bio-basecalling	Base-call raw ONT signals with Dorado/Guppy; convert FAST5 to FASTQ.
bio-compressed-files	Handle compressed bioinformatics files: bgzip, tabix, zstd, htslib.
bio-format-conversion	Convert between bioinformatics formats: FASTQ↔FASTA, BAM↔CRAM, BED↔GTF.
bio-sequence-statistics	Compute sequence statistics: GC content, length distributions, complexity.
bio-read-sequences	Read and iterate over biological sequences from FASTA/FASTQ files.
bio-write-sequences	Write biological sequences to FASTA/FASTQ with metadata preservation.
bio-filter-sequences	Filter sequences by length, quality, pattern, or taxonomy label.
bio-batch-processing	Batch-process large bioinformatics datasets across samples and cohorts.
bio-rnaseq-qc	RNA-seq specific QC: strandedness, rRNA contamination, gene body coverage.
bio-long-read-sequencing-clair3-variants	Call variants from long-read sequencing with Clair3 deep-learning model.
bio-long-read-sequencing-isoseq-analysis	Iso-Seq full-length transcript analysis for isoform discovery.
bio-long-read-sequencing-nanopore-methylation	Call CpG methylation from Oxford Nanopore sequencing with Modbam2bed.
bio-splicing-qc	RNA splicing quality assessment: junction read coverage, novel splice sites.
bio-splicing-quantification	Quantify alternative splicing events: PSI/inclusion levels per isoform.
bio-sashimi-plots	Generate sashimi plots for visualizing RNA-seq splicing at specific loci.
bio-consensus-sequences	Generate 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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Skill	Description
bio-de-deseq2-basics	DESeq2 differential expression analysis: design matrix, size factors, dispersion.
bio-de-edger-basics	EdgeR differential expression for count data with empirical Bayes dispersion.
bio-de-results	Extract, filter, and annotate DESeq2/EdgeR results tables.
bio-de-visualization	Volcano plots, MA plots, and heatmaps for differential expression results.
bio-differential-expression-batch-correction	Remove batch effects with ComBat/limma for multi-cohort DE analysis.
bio-differential-expression-timeseries-de	Time-series differential expression with splines and mixed models.
bio-differential-splicing	Detect differential alternative splicing events with rMATS or MAJIQ.
bio-isoform-switching	Identify isoform switching events with DRIMSeq and IsoformSwitchAnalyzeR.
bio-ribo-seq-orf-detection	Detect translated ORFs from ribosome profiling data with RiboTaper/Ribo-TISH.
bio-ribo-seq-riboseq-preprocessing	Preprocess ribosome profiling reads: adapter trimming, rRNA removal, alignment.
bio-ribo-seq-ribosome-periodicity	Assess triplet periodicity and ribosome footprint quality in Ribo-seq data.
bio-ribo-seq-ribosome-stalling	Identify ribosome stalling sites and pausing from Ribo-seq profiles.
bio-ribo-seq-translation-efficiency	Compute translation efficiency ratios from matched RNA-seq and Ribo-seq.

Bioinformatics — Pathway & Network Analysis

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Skill	Description
bio-pathway-go-enrichment	Gene Ontology enrichment analysis with clusterProfiler or g:Profiler.
bio-pathway-gsea	Gene Set Enrichment Analysis (GSEA) with pre-ranked or count-based statistics.
bio-pathway-kegg-pathways	KEGG pathway enrichment and visualization for metabolic/signaling pathways.
bio-pathway-reactome	Reactome pathway analysis with hierarchical enrichment and visualization.
bio-pathway-wikipathways	WikiPathways enrichment and network visualization.
bio-pathway-enrichment-visualization	Dot plots, enrichment maps, and network visualizations for pathway results.

Bioinformatics — Single-Cell & Spatial Omics

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Skill	Description
bio-single-cell-batch-integration	Integrate scRNA-seq datasets across batches with Harmony, BBKNN, scVI.
bio-single-cell-cell-annotation	Annotate single-cell clusters using marker genes and reference atlases.
bio-single-cell-cell-communication	Infer ligand-receptor cell-cell communication with CellChat or NicheNet.
bio-single-cell-clustering	Cluster single cells with Leiden/Louvain algorithms in Scanpy/Seurat.
bio-single-cell-data-io	Read/write AnnData, Seurat, and 10x Genomics h5ad/h5 formats.
bio-single-cell-doublet-detection	Remove doublets from scRNA-seq with Scrublet or DoubletFinder.
bio-single-cell-lineage-tracing	Reconstruct cell lineage trees from scRNA-seq with clonal barcodes.
bio-single-cell-markers-annotation	Identify cluster marker genes and auto-annotate cell types.
bio-single-cell-metabolite-communication	Infer metabolite-mediated intercellular communication from scRNA-seq.
bio-single-cell-multimodal-integration	Integrate scRNA-seq with ATAC, CITE-seq, or spatial using WNN/MultiVI.
bio-single-cell-perturb-seq	Analyze genetic perturbation screens from Perturb-seq / CROP-seq data.
bio-single-cell-preprocessing	Single-cell preprocessing: count filtering, normalization, HVG selection.
bio-single-cell-scatac-analysis	scATAC-seq peak calling, TF motif enrichment, and chromatin accessibility.
bio-single-cell-splicing	RNA velocity and splicing dynamics with scVelo or Alevin.
bio-single-cell-trajectory-inference	Infer pseudotime trajectories with Monocle3, PAGA, or Slingshot.
bio-spatial-transcriptomics-image-analysis	Analyze histology images co-registered with spatial transcriptomics data.
bio-spatial-transcriptomics-spatial-communication	Ligand-receptor communication analysis with spatial context (COMMOT, SpatialDE).
bio-spatial-transcriptomics-spatial-data-io	Load and process Visium, Slide-seq, MERFISH, and STARmap datasets.
bio-spatial-transcriptomics-spatial-deconvolution	Deconvolve cell type proportions in spatial spots with RCTD, SPOTlight.
bio-spatial-transcriptomics-spatial-domains	Identify spatially variable genes and tissue domains with SpatialDE/BANKSY.
bio-spatial-transcriptomics-spatial-multiomics	Integrate spatial transcriptomics with proteomics, metabolomics, or imaging.
bio-spatial-transcriptomics-spatial-neighbors	Build spatial neighbor graphs and perform neighborhood enrichment analysis.
bio-spatial-transcriptomics-spatial-preprocessing	Preprocess spatial transcriptomics: QC, normalization, spot filtering.
bio-spatial-transcriptomics-spatial-proteomics	Analyze spatial proteomics data from CODEX, IMC, or MIBI platforms.
bio-spatial-transcriptomics-spatial-statistics	Spatial statistics: Moran's I, spatial autocorrelation, co-localization.
bio-spatial-transcriptomics-spatial-visualization	Visualize spatial gene expression maps and tissue section overlays.

Bioinformatics — Epigenomics & Chromatin

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Skill	Description
bio-atac-seq-atac-peak-calling	Call ATAC-seq chromatin accessibility peaks with MACS2/MACS3.
bio-atac-seq-atac-qc	ATAC-seq quality control: TSS enrichment, fragment size, FRiP score.
bio-atac-seq-differential-accessibility	Differential chromatin accessibility between conditions with DESeq2/DiffBind.
bio-atac-seq-footprinting	Transcription factor footprinting from ATAC-seq with TOBIAS or HINT-ATAC.
bio-atac-seq-motif-deviation	TF motif deviation scoring with chromVAR for single-cell ATAC data.
bio-atac-seq-nucleosome-positioning	Infer nucleosome positioning from ATAC-seq fragment length distributions.
bio-chipseq-differential-binding	Differential ChIP-seq binding analysis with DiffBind.
bio-chipseq-motif-analysis	De novo and known motif discovery from ChIP-seq peaks with HOMER/MEME.
bio-chipseq-peak-annotation	Annotate ChIP-seq peaks with genomic features and nearest genes.
bio-chipseq-peak-calling	Call ChIP-seq peaks with MACS2 for TF binding and histone marks.
bio-chipseq-qc	ChIP-seq quality metrics: FRiP, SCC, phantompeakqualtools.
bio-chipseq-super-enhancers	Identify super enhancers from H3K27ac ChIP-seq with ROSE.
bio-chipseq-visualization	Heatmaps and aggregate profiles at peak regions with deepTools.
bio-hi-c-analysis-compartment-analysis	Call A/B compartments from Hi-C contact matrices.
bio-hi-c-analysis-contact-pairs	Process Hi-C contact pairs: filtering, deduplication, binning.
bio-hi-c-analysis-hic-data-io	Read and write Hi-C data formats: .hic, cool, mcool with cooler/hicstuff.
bio-hi-c-analysis-hic-differential	Differential Hi-C interaction analysis between conditions.
bio-hi-c-analysis-hic-visualization	Visualize Hi-C contact maps, TADs, and loops with pyGenomeTracks.
bio-hi-c-analysis-loop-calling	Detect chromatin loops from Hi-C data with Mustache or HICCUPS.
bio-hi-c-analysis-matrix-operations	Normalize Hi-C matrices: ICE, KR, VC; compute observed/expected.
bio-hi-c-analysis-tad-detection	Identify topologically associating domains (TADs) from Hi-C data.
bio-methylation-bismark-alignment	Align bisulfite sequencing reads and extract CpG methylation with Bismark.
bio-methylation-calling	Call CpG methylation from WGBS/RRBS alignments.
bio-methylation-dmr-detection	Identify differentially methylated regions (DMRs) with DSS or MethylKit.
bio-methylation-methylkit	Methylation analysis with MethylKit: CpG tiles, DMR calling, annotation.

Bioinformatics — Metagenomics & Microbiome

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Skill	Description
bio-metagenomics-abundance	Estimate microbial taxon abundances from shotgun metagenomics.
bio-metagenomics-amr-detection	Detect antimicrobial resistance genes with AMRFinder or RGI/CARD.
bio-metagenomics-functional-profiling	Functional profiling of metagenomes with HUMAnN3 for pathway/gene families.
bio-metagenomics-kraken	Taxonomic classification of metagenomic reads with Kraken2/Bracken.
bio-metagenomics-metaphlan	Clade-specific marker-based profiling of microbial communities with MetaPhlAn4.
bio-metagenomics-strain-tracking	Track microbial strains across samples with StrainPhlan or inStrain.
bio-metagenomics-visualization	Visualize microbiome composition with Krona charts and stacked bar plots.
bio-microbiome-amplicon-processing	Process 16S/ITS amplicon sequencing with QIIME2 or DADA2.
bio-microbiome-differential-abundance	Test differential microbial abundance with ANCOM-BC, MaAsLin2, or ALDEx2.
bio-microbiome-diversity-analysis	Alpha/beta diversity analysis: Shannon, PD, UniFrac, PCoA.
bio-microbiome-functional-prediction	Predict functional capacity from 16S data with PICRUSt2 or Tax4Fun.
bio-microbiome-qiime2-workflow	End-to-end QIIME2 workflow: denoising, diversity, differential abundance.
bio-microbiome-taxonomy-assignment	Assign taxonomy to ASVs/OTUs using SILVA, GTDB, or Greengenes2.

Bioinformatics — Immunoinformatics & Flow Cytometry

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Skill	Description
bio-immunoinformatics-epitope-prediction	Predict MHC-I/II epitopes from protein sequences with NetMHCpan/MHCflurry.
bio-immunoinformatics-immunogenicity-scoring	Score peptide immunogenicity for vaccine and neoantigen prioritization.
bio-immunoinformatics-mhc-binding-prediction	Predict peptide-MHC binding affinities for multiple alleles.
bio-immunoinformatics-neoantigen-prediction	Predict neoantigens from somatic mutations for personalized cancer vaccines.
bio-immunoinformatics-tcr-epitope-binding	Predict TCR-epitope binding with ERGO, pMTnet, or NetTCR.
bio-tcr-bcr-analysis-immcantation-analysis	Analyze B/T cell receptor repertoires with the Immcantation suite.
bio-tcr-bcr-analysis-mixcr-analysis	MiXCR V(D)J alignment and clonotype assembly for immune repertoires.
bio-tcr-bcr-analysis-repertoire-visualization	Visualize repertoire diversity, clonal expansion, and V-gene usage.
bio-tcr-bcr-analysis-scirpy-analysis	Single-cell TCR/BCR analysis integrated with scRNA-seq using Scirpy.
bio-tcr-bcr-analysis-vdjtools-analysis	Immune repertoire statistics and overlap analysis with VDJtools.
bio-flow-cytometry-bead-normalization	Normalize flow cytometry data using calibration beads.
bio-flow-cytometry-clustering-phenotyping	Cluster and phenotype cell populations with FlowSOM, PhenoGraph, or UMAP.
bio-flow-cytometry-compensation-transformation	Apply compensation matrices and biexponential/arcsinh transformations.
bio-flow-cytometry-cytometry-qc	Quality control for flow/mass cytometry: signal drift, spillover, outlier detection.
bio-flow-cytometry-differential-analysis	Statistical comparison of cell populations between conditions.
bio-flow-cytometry-doublet-detection	Detect and remove doublets from flow cytometry data.
bio-flow-cytometry-fcs-handling	Read, write, and manipulate FCS files with FlowCore/FlowKit.
bio-flow-cytometry-gating-analysis	Manual and algorithmic gating strategies for cell population identification.
bio-imaging-mass-cytometry-cell-segmentation	Segment cells in IMC images with Mesmer or CellProfiler.
bio-imaging-mass-cytometry-data-preprocessing	Preprocess imaging mass cytometry data: hot pixel removal, normalization.
bio-imaging-mass-cytometry-interactive-annotation	Interactively annotate cell types in IMC spatial datasets.
bio-imaging-mass-cytometry-phenotyping	Phenotype immune and tumor cells from multi-marker IMC panels.
bio-imaging-mass-cytometry-quality-metrics	Quality metrics for IMC acquisitions: signal-to-noise, tissue coverage.
bio-imaging-mass-cytometry-spatial-analysis	Spatial cell neighborhood analysis from imaging mass cytometry data.

Bioinformatics — Multi-Omics Integration

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Skill	Description
bio-multi-omics-data-harmonization	Harmonize multi-omics datasets: sample matching, batch correction, feature alignment.
bio-multi-omics-mixomics-analysis	Multi-omics factor analysis with mixOmics (DIABLO, MOFA, sPLS-DA).
bio-multi-omics-mofa-integration	Multi-Omics Factor Analysis (MOFA+) for latent factor discovery across modalities.
bio-multi-omics-similarity-network	Similarity Network Fusion (SNF) for patient stratification from multi-omics.

Bioinformatics — Proteomics & Metabolomics

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Skill	Description
bio-proteomics-data-import	Import DDA/DIA proteomics data from MaxQuant, Proteome Discoverer, FragPipe.
bio-proteomics-dia-analysis	DIA proteomics analysis with DIA-NN or Spectronaut.
bio-proteomics-differential-abundance	Differential protein abundance with limma, MSstats, or DEqMS.
bio-proteomics-peptide-identification	Peptide spectrum matching and database search result parsing.
bio-proteomics-protein-inference	Protein grouping, parsimony, and FDR control for proteomics experiments.
bio-proteomics-proteomics-qc	Proteomics QC: peptide counts, coverage, missing values, CV.
bio-proteomics-ptm-analysis	Post-translational modification analysis: phospho, ubiquitin, glycan enrichment.
bio-proteomics-quantification	Label-free, TMT/iTRAQ, and SILAC quantification workflows.
bio-proteomics-spectral-libraries	Build and use spectral libraries for DIA data analysis.
bio-metabolomics-lipidomics	Lipidomics data analysis: lipid class annotation, fatty acid composition.
bio-metabolomics-metabolite-annotation	Annotate mass spec features with HMDB, MZmine, SIRIUS, or MetFrag.
bio-metabolomics-msdial-preprocessing	MS-DIAL-based LC-MS/GC-MS data preprocessing and peak detection.
bio-metabolomics-normalization-qc	Metabolomics normalization: PQN, LOESS, median, batch correction.
bio-metabolomics-pathway-mapping	Map identified metabolites to KEGG, MetaCyc, or Reactome pathways.
bio-metabolomics-statistical-analysis	Univariate/multivariate stats for metabolomics: PCA, PLS-DA, ANOVA.
bio-metabolomics-targeted-analysis	Targeted metabolomics with MRM/SRM: calibration curves, quantification.
bio-metabolomics-xcms-preprocessing	XCMS-based LC-MS peak detection, alignment, and grouping.

Bioinformatics — Structural Biology & Cheminformatics

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Skill	Description
bio-structural-biology-alphafold-predictions	Use AlphaFold2/3 predictions: model quality assessment, confidence scores.
bio-structural-biology-modern-structure-prediction	Modern structure prediction with ESMFold, RoseTTAFold, and OpenFold.
bio-pdb-geometric-analysis	Geometric analysis of protein structures: distances, angles, contacts, RMSD.
bio-pdb-structure-io	Read and write PDB/mmCIF structure files with BioPython or Gemmi.
bio-pdb-structure-modification	Modify protein structures: add hydrogens, mutate residues, energy minimize.
bio-pdb-structure-navigation	Navigate and inspect PDB structures: chain, residue, atom selection.
bio-molecular-descriptors	Calculate molecular descriptors (RDKit): MW, LogP, TPSA, fingerprints.
bio-molecular-io	Read/write chemical structure formats: SDF, SMILES, MOL2, PDB with RDKit.
bio-reaction-enumeration	Enumerate reactions and products from SMARTS reaction templates.
bio-similarity-searching	Molecular similarity search: Tanimoto, fingerprint-based, scaffold hopping.
bio-substructure-search	Substructure searching in chemical databases using SMARTS patterns.
bio-virtual-screening	Virtual screening workflows: docking, scoring, pose filtering with AutoDock/Vina.
bio-admet-prediction	Predict ADMET properties: absorption, distribution, metabolism, excretion, toxicity.

Bioinformatics — Epidemiological & Causal Genomics

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Skill	Description
bio-epidemiological-genomics-amr-surveillance	Antimicrobial resistance surveillance from genomic epidemiology data.
bio-epidemiological-genomics-pathogen-typing	Pathogen molecular typing: MLST, wgMLST, cgMLST for outbreak analysis.
bio-epidemiological-genomics-phylodynamics	Phylodynamics: molecular clock, population dynamics, BEAST2/TreeTime.
bio-epidemiological-genomics-transmission-inference	Infer transmission networks from pathogen genomics with TransPhylo/outbreaker2.
bio-epidemiological-genomics-variant-surveillance	Track pathogen variant emergence and spread from genomic surveillance.
bio-causal-genomics-colocalization-analysis	Colocalization analysis of GWAS and eQTL signals with coloc or eCAVIAR.
bio-causal-genomics-fine-mapping	Fine-map causal variants at GWAS loci with SuSiE or FINEMAP.
bio-causal-genomics-mediation-analysis	Causal mediation analysis for gene expression intermediaries.
bio-causal-genomics-mendelian-randomization	Two-sample Mendelian randomization with MR-Base/TwoSampleMR.
bio-causal-genomics-pleiotropy-detection	Detect horizontal pleiotropy and heterogeneity in MR analyses.
bio-genome-engineering-base-editing-design	Design base editors (CBE/ABE) for precise single-base correction.
bio-genome-engineering-grna-design	Design and score CRISPR guide RNAs with Cas-OFFinder and CRISPOR.
bio-genome-engineering-hdr-template-design	Design HDR templates for precise knock-in via homology-directed repair.
bio-genome-engineering-off-target-prediction	Predict CRISPR off-target sites genome-wide for safety assessment.
bio-genome-engineering-prime-editing-design	Design pegRNAs and nickase gRNAs for prime editing experiments.
bio-crispr-screens-base-editing-analysis	Analyze base editing screens: guide efficiency, editing outcomes.
bio-crispr-screens-batch-correction	Correct batch effects in CRISPR screen data across replicates.
bio-crispr-screens-crispresso-editing	Quantify editing outcomes with CRISPResso2 from amplicon sequencing.
bio-crispr-screens-hit-calling	Call hits from CRISPR screens using MAGeCK, BAGEL2, or casTLE.
bio-crispr-screens-jacks-analysis	CRISPR screen analysis with JACKS hierarchical Bayesian model.
bio-crispr-screens-library-design	Design CRISPR screen libraries: guide selection, controls, coverage.
bio-crispr-screens-mageck-analysis	MAGeCK MLE/RRA analysis for CRISPR pooled screens.
bio-crispr-screens-screen-qc	Quality control for CRISPR screens: Gini index, read distribution.

🔬 Omics & Computational Biology

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Single-Cell & Spatial Omics

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Skill	Description
anndata	Working with annotated data matrices in Python for single-cell genomics analysis, managing experimental measurements with metadata and large-scale omics data.
scanpy	Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory.
scvi-tools	Deep 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-qc	Quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
cellxgene-census	Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
pydeseq2	Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots.
bulk-combat-correction	Remove batch effects from merged bulk RNA-seq or microarray cohorts using pyComBat, with corrected matrix export and pre/post correction visualizations.
bulk-deg-analysis	Bulk RNA-seq DEG pipeline: gene ID mapping, DESeq2 normalization, statistical testing, visualization, and pathway enrichment via OmicVerse.
bulk-deseq2-analysis	PyDESeq2-based differential expression analysis with ID mapping, DE testing, fold-change thresholding, and enrichment visualization.
bulk-stringdb-ppi	Query STRING for protein interactions, build PPI graphs with pyPPI, and render network figures for bulk gene lists.
bulk-to-single-deconvolution	Convert bulk RNA-seq cohorts to synthetic single-cell datasets using Bulk2Single workflow for cell fraction estimation and beta-VAE generation.
bulk-trajblend-interpolation	Extend scRNA-seq developmental trajectories with BulkTrajBlend by generating intermediate cells from bulk RNA-seq using beta-VAE and GNN models.
bulk-wgcna-analysis	Run PyWGCNA through OmicVerse — co-expression module construction, eigengene visualization, and hub gene extraction.
single-annotation	Single-cell annotation workflows: SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer for annotating cell types across modalities.
single-cellphone-db	Run CellPhoneDB v5 on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualizations.
single-clustering	Single-cell clustering workflow: QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration in OmicVerse.
single-downstream-analysis	OmicVerse downstream tutorials covering AUCell scoring, metacell DEG, and related exports for single-cell data.
single-multiomics	OmicVerse multi-omics tutorials: MOFA, GLUE pairing, SIMBA integration, TOSICA transfer, and StaVIA cartography.
single-preprocessing	Single-cell preprocessing in OmicVerse: QC, normalization, HVG detection, PCA/embedding pipelines (CPU/GPU).
single-to-spatial-mapping	Map scRNA-seq atlases onto spatial transcriptomics slides using Single2Spatial workflow for deep-forest training and marker visualization.
single-trajectory	OmicVerse trajectory workflows: PAGA, Palantir, VIA, velocity coupling, and fate scoring.
spatial-tutorials	Spatial transcriptomics tutorials: preprocessing, deconvolution, and downstream modeling across Visium, Visium HD, Stereo-seq, and Slide-seq.
tcga-preprocessing	Ingest TCGA sample sheets, expression archives, and clinical carts into OmicVerse, with survival metadata initialization and AnnData export.
gsea-enrichment	Gene set enrichment analysis in OmicVerse with correct geneset format handling for loading pathway databases and running GSEA.

Cheminformatics & Drug Discovery

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Skill	Description
rdkit	Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity.
datamol	Pythonic RDKit wrapper with simplified interface for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformer generation.
medchem	Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
diffdock	Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.
molfeat	Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
deepchem	Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, for drug discovery ML.
torchdrug	Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs.
torch_geometric	Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, molecular property prediction, for geometric deep learning in drug discovery.
pytdc	Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML.
cobrapy	Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering.

Proteomics & Mass Spectrometry

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Skill	Description
matchms	Mass spectrometry spectral analysis. Process mzML/MGF/MSP files, spectral similarity (cosine, modified cosine), metadata harmonization, compound identification.
pyopenms	Python interface to OpenMS for LC-MS/MS proteomics and metabolomics workflows. File handling (mzML, mzXML, mzTab, pepXML, mzIdentML) and quantification.
flowio	Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

Protein Structure & Design

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Skill	Description
esm	ESM3 generative multimodal protein design (sequence, structure, function) and ESM C efficient protein embeddings. Protein language models for sequence scoring and embedding.
alphafold	Validate protein designs using AlphaFold2 structure prediction. Validates designed sequences, predicts binder-target complex structures, calculates pLDDT/PAE metrics.
boltz	Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor for protein complexes, binder validation, and open-source AlphaFold alternative.
boltzgen	All-atom protein design using BoltzGen diffusion model. Side-chain aware design from the start, designing around small molecules or ligands.
chai	Structure prediction using Chai-1 foundation model for protein-protein complexes, binder validation, and protein-small molecule interaction prediction.
rfdiffusion	Generate protein backbones using RFdiffusion diffusion model for de novo protein structure generation and binder scaffold design.
bindcraft	End-to-end binder design using BindCraft hallucination with built-in AF2 validation for production-quality binder campaigns.
binder-design	Guidance for choosing the right protein binder design tool (BoltzGen, BindCraft, or RFdiffusion) and planning binder design campaigns.
proteinmpnn	Design protein sequences using ProteinMPNN inverse folding for RFdiffusion backbones, sequence redesign, and partial fixed-position design.
ligandmpnn	Ligand-aware protein sequence design using LigandMPNN for sequences around small molecules, enzyme active site design, and binding pocket optimization.
solublempnn	Solubility-optimized protein sequence design using SolubleMPNN for E. coli expression, reducing aggregation, and solubility optimization.
foldseek	Structure similarity search with Foldseek for finding similar structures in PDB/AFDB databases, structural homology search, and evolutionary relationship discovery.
ipsae	Binder design ranking using ipSAE (interprotein Score from Aligned Errors) for ranking binder designs and filtering BindCraft or RFdiffusion outputs.
pdb	Fetch and analyze protein structures from RCSB PDB by PDB ID, search for similar structures, prepare targets for binder design.
protein-design-workflow	End-to-end guidance for protein design pipelines from project initiation to experimental validation.
protein-qc	Quality control metrics and filtering thresholds for protein design: pLDDT, PAE, ipTM for binding, expression, and structure evaluation.
cell-free-expression	Guidance for cell-free protein synthesis (CFPS) optimization, troubleshooting low yield/aggregation, and optimizing DNA template design.
binding-characterization	Guidance for SPR and BLI binding characterization experiments, kinetics interpretation, and troubleshooting poor binding signal.

Single-Cell & Trajectory Analysis

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Skill	Description
scvelo	RNA velocity analysis. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in scRNA-seq data.

Phylogenetics & Network Analysis

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Skill	Description
phylogenetics	Build and analyze phylogenetic trees using MAFFT, IQ-TREE 2, and FastTree. Evolutionary analysis, microbial genomics, viral phylodynamics, and molecular clock studies.
networkx	Network and graph analysis in Python. Biological network analysis, protein interaction networks, pathway graphs, community detection, and centrality measures.
torch-geometric	Graph Neural Networks (PyG) for molecular property prediction, drug-target interaction modeling, and geometric deep learning on biological graphs.

⚙️ ClawBio Pipelines

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Bioinformatics Orchestration & Pipelines (ClawBio)

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Skill	Description
bio-orchestrator	Meta-agent routing bioinformatics requests to specialized sub-skills. Handles file type detection (VCF, FASTQ, BAM, PDB, h5ad), analysis planning, report generation, and reproducibility export.
scrna-orchestrator	Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and two-group differential expression from raw-count .h5ad files.
seq-wrangler	Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
vcf-annotator	Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritized variant reports.
repro-enforcer	Export bioinformatics analyses as reproducible bundles with Conda environment, Singularity container definition, and Nextflow pipeline.
galaxy-bridge	Galaxy tool discovery, recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions.

Genomics, Ancestry & Pharmacogenomics (ClawBio)

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Skill	Description
gwas-lookup	Federated variant lookup across 9 genomic databases: GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.
gwas-prs	Calculate polygenic risk scores from DTC genetic data (23andMe/AncestryDNA) using the PGS Catalog.
pharmgx-reporter	Pharmacogenomic report from DTC genetic data — 12 genes, 31 SNPs, 51 drugs with CPIC guidelines and personalized dosage cards.
clinpgx	Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels.
drug-photo	Identify a medication from a packaging photo via Claude vision, then retrieve genotype-informed dosage guidance.
claw-ancestry-pca	Ancestry decomposition PCA against the Simons Genome Diversity Project (345 samples, 164 global populations).
genome-compare	Compare genome to reference individuals and estimate ancestry composition via IBS and EM admixture.
equity-scorer	Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and HEIM Equity Score with markdown reports.
claw-metagenomics	Shotgun metagenomics profiling: taxonomy (Kraken2/Bracken), resistome (CARD/RGI), and functional pathways (HUMAnN3) from paired-end FASTQ.
ukb-navigator	Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.

Structural Biology & Literature (ClawBio)

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Skill	Description
struct-predictor	Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare structures, compute RMSD, visualize 3D models.
lit-synthesizer	Search PubMed and bioRxiv, summarize papers with LLM, build citation graphs, and generate literature review sections.
claw-semantic-sim	Semantic Similarity Index for disease research literature using PubMedBERT embeddings. Compute research equity metrics (HEIM).
labstep	Interact with the Labstep electronic lab notebook API. Query experiments, protocols, resources, and inventory.
profile-report	Generate structured bioinformatics analysis profile reports.

🧠 BioOS Extended Suite

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BioOS Extended Bioinformatics Suite (mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-)

Sequence & Alignment Tools

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Skill	Description
bio-alignment-sorting	Sort SAM/BAM files by coordinate or name with samtools sort.
bio-alignment-filtering	Filter alignments by flag, quality, region, or paired status.
bio-alignment-indexing	Index BAM/CRAM files with samtools index for random access.
bio-alignment-validation	Validate alignment file integrity and detect truncated/corrupt files.
bio-alignment-files-bam-statistics	Compute alignment statistics: flagstat, idxstats, coverage depth.
bio-sam-bam-basics	Read, inspect, and manipulate SAM/BAM files with samtools/pysam.
bio-duplicate-handling	Mark and remove PCR duplicates with Picard or samtools markdup.
bio-pileup-generation	Generate base-level pileup from BAM for variant calling and coverage.
bio-reference-operations	Download, index, and manage reference genome FASTA files.
bio-blast-searches	Run BLAST searches against local or remote databases for sequence homology.
bio-local-blast	Set up and run BLAST+ locally with custom databases.
bio-entrez-search	Search NCBI Entrez databases (PubMed, gene, nucleotide, protein, SRA).
bio-entrez-fetch	Fetch records from NCBI Entrez by accession or UID.
bio-entrez-link	Retrieve linked records across NCBI Entrez databases.
bio-uniprot-access	Query UniProt for protein sequences, annotations, and cross-references.
bio-geo-data	Download and parse GEO datasets and series matrices.
bio-sra-data	Download raw sequencing data from NCBI SRA with fasterq-dump.
bio-batch-downloads	Batch download bioinformatics data from NCBI, EBI, Ensembl.

Sequence Analysis

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Skill	Description
bio-seq-objects	Work with BioPython sequence objects: SeqRecord, features, annotations.
bio-sequence-properties	Compute sequence properties: MW, pI, hydrophobicity, extinction coefficient.
bio-sequence-similarity	Compute sequence similarity with pairwise alignment and percent identity.
bio-sequence-slicing	Slice, extract, and manipulate subsequences from FASTA/FASTQ.
bio-motif-search	Search sequences for regulatory motifs using FIMO, MAST, or regex.
bio-codon-usage	Analyze codon usage bias and optimize sequences for expression.
bio-transcription-translation	Transcribe and translate DNA sequences; handle genetic code variations.
bio-reverse-complement	Compute reverse complement and strand-aware sequence operations.
bio-primer-design-primer-basics	Design PCR primers with Primer3 for standard amplification.
bio-primer-design-primer-validation	Validate primer specificity by BLAST and thermodynamic analysis.
bio-primer-design-qpcr-primers	Design qPCR/RT-PCR primers with efficiency and specificity optimization.
bio-restriction-sites	Find restriction enzyme recognition sites in DNA sequences.
bio-restriction-mapping	Create restriction maps and in silico digestion patterns.
bio-restriction-fragment-analysis	Analyze restriction fragment patterns for cloning and gel prediction.
bio-restriction-enzyme-selection	Select restriction enzymes for cloning based on cut sites and compatibility.

Read Alignment

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Skill	Description
bio-read-alignment-bwa-alignment	Align short reads to reference genome with BWA-MEM.
bio-read-alignment-bowtie2-alignment	Align short reads with Bowtie2; local and end-to-end modes.
bio-read-alignment-hisat2-alignment	Splice-aware RNA-seq alignment with HISAT2.
bio-read-alignment-star-alignment	High-speed STAR aligner for RNA-seq with junction detection.

Genome Assembly

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Skill	Description
bio-genome-assembly-long-read-assembly	De novo assembly from ONT/PacBio long reads with Flye or Canu.
bio-genome-assembly-hifi-assembly	HiFi (CCS) read assembly with Hifiasm for high-accuracy genomes.
bio-genome-assembly-short-read-assembly	Illumina de novo assembly with SPAdes for metagenomes/bacteria/transcriptomes.
bio-genome-assembly-metagenome-assembly	Metagenomic assembly: co-assembly, binning, MAG recovery.
bio-genome-assembly-assembly-qc	Assess assembly quality with QUAST, BUSCO, and NGA50 metrics.
bio-genome-assembly-assembly-polishing	Polish assemblies with Medaka (ONT) or NextPolish (Illumina).
bio-genome-assembly-scaffolding	Scaffold contigs with Hi-C, optical mapping, or long reads.
bio-genome-assembly-contamination-detection	Detect and remove contamination in assembled genomes.

Genome Intervals & Annotation

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Skill	Description
bio-genome-intervals-bed-file-basics	Read, write, and filter BED files with pybedtools/bedtools.
bio-genome-intervals-interval-arithmetic	Intersect, subtract, merge, and complement genomic intervals.
bio-genome-intervals-proximity-operations	Find nearest features and compute distances between intervals.
bio-genome-intervals-coverage-analysis	Compute read depth coverage across genomic regions.
bio-genome-intervals-bigwig-tracks	Create and query BigWig signal tracks from BAM/bedGraph.
bio-genome-intervals-gtf-gff-handling	Parse and manipulate GTF/GFF annotation files.
bio-bedgraph-handling	Process bedGraph coverage files: arithmetic, normalization, conversion.

RNA Quantification

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Skill	Description
bio-rna-quantification-featurecounts-counting	Count reads per gene with featureCounts from subread package.
bio-rna-quantification-alignment-free-quant	Pseudo-alignment quantification with Salmon or Kallisto.
bio-rna-quantification-tximport-workflow	Import Salmon/Kallisto quantification into R/DESeq2 with tximport.
bio-rna-quantification-count-matrix-qc	QC count matrices: library size, zero inflation, gene detection rates.
bio-expression-matrix-counts-ingest	Load and validate count matrices from multiple quantification tools.
bio-expression-matrix-gene-id-mapping	Map between Ensembl, Entrez, HGNC, and gene symbol identifiers.
bio-expression-matrix-metadata-joins	Join sample metadata to expression matrices for downstream analysis.
bio-expression-matrix-sparse-handling	Handle sparse count matrices efficiently with scipy sparse formats.

Epitranscriptomics & CLIP-seq

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Skill	Description
bio-epitranscriptomics-merip-preprocessing	Preprocess MeRIP-seq data for m6A methylation analysis.
bio-epitranscriptomics-m6a-peak-calling	Call m6A peaks from MeRIP-seq with exomePeak2 or MACS2.
bio-epitranscriptomics-m6anet-analysis	Nanopore direct RNA m6A detection with m6Anet deep learning.
bio-epitranscriptomics-m6a-differential	Differential m6A methylation analysis between conditions.
bio-epitranscriptomics-modification-visualization	Visualize RNA modification profiles and metagene plots.
bio-clip-seq-clip-preprocessing	Preprocess CLIP-seq/eCLIP data: adapter trimming, demultiplexing.
bio-clip-seq-clip-alignment	Align CLIP-seq reads with STAR; handle unique mappers.
bio-clip-seq-clip-peak-calling	Call RBP binding peaks from CLIP-seq with PureCLIP or MACS2.
bio-clip-seq-binding-site-annotation	Annotate CLIP-seq peaks with genomic features and RNA regions.
bio-clip-seq-clip-motif-analysis	Discover RBP binding motifs from CLIP-seq peak sequences.

Small RNA-seq

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Skill	Description
bio-small-rna-seq-smrna-preprocessing	Preprocess small RNA-seq: adapter trimming, size selection.
bio-small-rna-seq-mirdeep2-analysis	Identify and quantify known/novel miRNAs with miRDeep2.
bio-small-rna-seq-mirge3-analysis	miRNA annotation and quantification with miRge3.0.
bio-small-rna-seq-target-prediction	Predict miRNA target genes with TargetScan or miRDB.
bio-small-rna-seq-differential-mirna	Differential miRNA expression analysis with DESeq2/edgeR.

Population Genetics & Phasing

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Skill	Description
bio-population-genetics-plink-basics	PLINK2 for GWAS QC, LD pruning, and basic population genetics.
bio-population-genetics-population-structure	Population stratification with PCA, ADMIXTURE, and STRUCTURE.
bio-population-genetics-linkage-disequilibrium	Compute LD metrics (r², D') and LD decay analysis.
bio-population-genetics-association-testing	GWAS association testing with PLINK, BOLT-LMM, or SAIGE.
bio-population-genetics-scikit-allel-analysis	Population genetics analysis with scikit-allel: diversity, Fst, haplotypes.
bio-population-genetics-selection-statistics	Detect natural selection signatures: iHS, XP-EHH, Tajima's D.
bio-phasing-imputation-haplotype-phasing	Phase variants with SHAPEIT4 or BEAGLE.
bio-phasing-imputation-genotype-imputation	Impute missing genotypes using Michigan/TOPMed imputation servers.
bio-phasing-imputation-reference-panels	Select and prepare reference panels (1KGP, HRC, TOPMed) for imputation.
bio-phasing-imputation-imputation-qc	QC imputed data: R² filter, INFO score, allele concordance.

Comparative Genomics & Phylogenetics

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Skill	Description
bio-comparative-genomics-ortholog-inference	Infer orthologs and paralogs with OrthoFinder or OMA.
bio-comparative-genomics-synteny-analysis	Detect syntenic blocks between genomes with MCScan or SyRI.
bio-comparative-genomics-positive-selection	Test for positive selection with PAML, HyPhy, or dN/dS ratios.
bio-comparative-genomics-hgt-detection	Detect horizontal gene transfer events in microbial genomes.
bio-comparative-genomics-ancestral-reconstruction	Reconstruct ancestral sequences and traits with ASR methods.
bio-phylo-tree-io	Read/write phylogenetic trees in Newick, Nexus, PhyloXML formats.
bio-phylo-modern-tree-inference	Maximum likelihood tree inference with IQ-TREE 2 or FastTree.
bio-phylo-tree-manipulation	Root, prune, reorder, and annotate phylogenetic trees.
bio-phylo-tree-visualization	Visualize trees with iTOL, ETE3, or ggtree.
bio-phylo-distance-calculations	Compute pairwise phylogenetic distances and diversity metrics.

Systems Biology & Metabolic Modeling

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Skill	Description
bio-systems-biology-flux-balance-analysis	Flux balance analysis (FBA) with COBRApy for metabolic network modeling.
bio-systems-biology-metabolic-reconstruction	Reconstruct genome-scale metabolic models from genome annotations.
bio-systems-biology-gene-essentiality	Predict essential genes by single gene knockouts in metabolic models.
bio-systems-biology-context-specific-models	Build context-specific metabolic models from expression data (GIMME, iMAT).
bio-systems-biology-model-curation	Curate SBML metabolic models: mass/charge balance, gap filling.

Experimental Design & Reporting

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Skill	Description
bio-experimental-design-sample-size	Power analysis and sample size calculation for omics experiments.
bio-experimental-design-power-analysis	Statistical power analysis for detecting differential signals.
bio-experimental-design-batch-design	Optimize sample batching to minimize confounding with ComBat design.
bio-experimental-design-multiple-testing	Multiple testing correction: Bonferroni, BH/FDR, q-values.
bio-machine-learning-omics-classifiers	Train classifiers on omics data: random forest, SVM, XGBoost.
bio-machine-learning-biomarker-discovery	Identify biomarkers from omics data with LASSO, elastic net, SHAP.
bio-machine-learning-model-validation	Cross-validation, AUC-ROC, calibration, and permutation testing.
bio-machine-learning-survival-analysis	Survival ML: RSF, DeepSurv, CoxBoost from omics features.
bio-machine-learning-atlas-mapping	Map query cells to reference atlases with scANVI or Symphony.
bio-machine-learning-prediction-explanation	Explain omics ML predictions with SHAP and feature importance.
bio-reporting-automated-qc-reports	Generate automated MultiQC-style reports for omics pipelines.
bio-reporting-jupyter-reports	Create Jupyter notebook reports with reproducible analysis code.
bio-reporting-rmarkdown-reports	Render Rmarkdown reports with integrated plots and statistics.
bio-reporting-quarto-reports	Build Quarto multi-format reports (HTML/PDF) from analysis code.
bio-reporting-figure-export	Export publication-quality figures in PDF/SVG/TIFF at specified DPI.
bio-research-tools-biomarker-signature-studio	Build, validate, and visualize multi-omic biomarker signatures.

End-to-End Workflow Pipelines

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Skill	Description
bio-workflows-fastq-to-variants	Complete FASTQ → alignment → variant calling pipeline.
bio-workflows-rnaseq-to-de	RNA-seq → alignment → counts → DESeq2 differential expression.
bio-workflows-scrnaseq-pipeline	Single-cell RNA-seq end-to-end: Cell Ranger → Scanpy → clustering.
bio-workflows-atacseq-pipeline	ATAC-seq: trimming → alignment → peak calling → differential.
bio-workflows-chipseq-pipeline	ChIP-seq: alignment → peak calling → motif analysis → annotation.
bio-workflows-methylation-pipeline	WGBS/RRBS: bismark alignment → methylation calling → DMR detection.
bio-workflows-metagenomics-pipeline	Metagenomics: QC → classification → functional profiling → AMR.
bio-workflows-metabolomics-pipeline	LC-MS/GC-MS: preprocessing → annotation → statistical analysis.
bio-workflows-proteomics-pipeline	DDA/DIA proteomics: search → quantification → differential abundance.
bio-workflows-gwas-pipeline	GWAS: QC → imputation → association → fine-mapping → annotation.
bio-workflows-somatic-variant-pipeline	Tumor-normal somatic variant calling with GATK Mutect2/Strelka2.
bio-workflows-cnv-pipeline	Copy number variant detection: WGS/WES CNV calling and annotation.
bio-workflows-spatial-pipeline	Spatial transcriptomics: alignment → deconvolution → domain detection.
bio-workflows-multi-omics-pipeline	Multi-omics integration pipeline: MOFA, SNF, similarity network fusion.
bio-workflows-multiome-pipeline	10x Multiome: joint scRNA-seq + scATAC-seq processing and integration.
bio-workflows-hic-pipeline	Hi-C contact map generation, normalization, TAD/loop calling.
bio-workflows-neoantigen-pipeline	Neoantigen prediction: somatic variants → MHC binding → immunogenicity.
bio-workflows-microbiome-pipeline	Microbiome: 16S/ITS amplicon or shotgun → diversity → differential.
bio-workflows-crispr-screen-pipeline	CRISPR screen: guide counting → MAGeCK → hit calling → visualization.
bio-workflows-crispr-editing-pipeline	CRISPR editing: amplicon sequencing → CRISPResso2 → outcome analysis.
bio-workflows-tcr-pipeline	TCR/BCR: V(D)J alignment → clonotype → repertoire analysis.
bio-workflows-riboseq-pipeline	Ribo-seq: footprint alignment → periodicity → ORF detection.
bio-workflows-smrna-pipeline	Small RNA-seq: miRNA identification → quantification → DE analysis.
bio-workflows-merip-pipeline	MeRIP-seq: m6A peak calling → differential → motif analysis.
bio-workflows-clip-pipeline	CLIP-seq: peak calling → binding site annotation → motif discovery.
bio-workflows-imc-pipeline	Imaging mass cytometry: segmentation → phenotyping → spatial analysis.
bio-workflows-cytometry-pipeline	Flow/mass cytometry: QC → gating → clustering → differential.
bio-workflows-longread-sv-pipeline	Long-read structural variant calling and annotation pipeline.
bio-workflows-genome-assembly-pipeline	De novo genome assembly: raw reads → assembly → QC → annotation.
bio-workflows-outbreak-pipeline	Pathogen genomics: assembly → typing → phylodynamics → transmission.
bio-workflows-biomarker-pipeline	Biomarker discovery: omics → feature selection → validation → report.
bio-workflows-metabolic-modeling-pipeline	Metabolic model reconstruction → FBA → simulation → visualization.
bio-splicing-pipeline	Alternative splicing analysis: rMATS → PSI → differential → sashimi.
bio-liquid-biopsy-pipeline	Liquid biopsy: cfDNA/ctDNA QC → mutation detection → TMB → MRD.
bio-workflow-management-snakemake-workflows	Create and manage Snakemake reproducible bioinformatics workflows.
bio-workflow-management-nextflow-pipelines	Build and run Nextflow (DSL2) bioinformatics pipelines.
bio-workflow-management-cwl-workflows	Write Common Workflow Language (CWL) portable workflow definitions.
bio-workflow-management-wdl-workflows	Create WDL workflows for Terra/Cromwell bioinformatics execution.
bio-workflows-expression-to-pathways	End-to-end workflow from differential expression to GO/KEGG/Reactome enrichment and pathway visualization.

Data Visualization (Bioinformatics)

Click to expand skill list

Skill	Description
bio-data-visualization-heatmaps-clustering	Hierarchical clustering heatmaps with ComplexHeatmap or seaborn.
bio-data-visualization-volcano-customization	Customized volcano plots with ggplot2 or matplotlib for DE results.
bio-data-visualization-circos-plots	Circular genome visualization with Circos or pycirclize.
bio-data-visualization-genome-browser-tracks	Generate genome browser tracks and IGV sessions from BAM/BigWig.
bio-data-visualization-genome-tracks	Multi-panel genome track plots with pyGenomeTracks.
bio-data-visualization-ggplot2-fundamentals	R ggplot2 for publication-quality genomics and omics figures.
bio-data-visualization-interactive-visualization	Interactive omics visualizations with Plotly, Bokeh, or shiny.
bio-data-visualization-upset-plots	UpSet plots for multi-set intersection visualization.
bio-data-visualization-multipanel-figures	Compose multipanel publication figures with cowplot or patchwork.
bio-data-visualization-color-palettes	Scientific color palettes: colorblind-safe, perceptually uniform, diverging.
bio-data-visualization-specialized-omics-plots	Specialized plots: lollipop (mutations), circomap, oncoprint.

Oncology & Precision Medicine Agents (BioOS)

Click to expand skill list

Skill	Description
autonomous-oncology-agent	Autonomous oncology research agent: literature mining, trial matching, biomarker analysis, and treatment hypothesis generation.
precision-oncology-agent	Precision oncology: tumor molecular profiling → actionable alterations → treatment recommendations.
pan-cancer-multiomics-agent	Pan-cancer multi-omics integration for cross-cancer pattern discovery and driver identification.
tumor-clonal-evolution-agent	Model tumor clonal evolution: phylogenetic trees, clonal dynamics, branching patterns from somatic variants.
tumor-heterogeneity-agent	Analyze intratumoral heterogeneity from bulk and single-cell sequencing data.
tumor-mutational-burden-agent	Compute TMB and assess its predictive value for immunotherapy response.
chromosomal-instability-agent	Quantify chromosomal instability (CIN) from copy number and SV data.
cancer-metabolism-agent	Analyze tumor metabolic reprogramming from transcriptomic and metabolomic data.
liquid-biopsy-analytics-agent	Comprehensive liquid biopsy analytics: ctDNA detection, MRD monitoring, treatment response.
ctdna-dynamics-mrd-agent	Track ctDNA dynamics for minimal residual disease detection and treatment monitoring.
mrd-edge-detection-agent	Ultra-sensitive MRD detection from deep sequencing with error suppression.
hrd-analysis-agent	Homologous recombination deficiency (HRD) analysis for PARP inhibitor response prediction.
computational-pathology-agent	Computational pathology: WSI analysis, tissue segmentation, histological feature extraction.
multimodal-radpath-fusion-agent	Fuse radiology and pathology imaging for integrated cancer phenotyping.
radiomics-pathomics-fusion-agent	Extract radiomic and pathomic features and integrate for predictive modeling.
radgpt-radiology-reporter	AI-assisted radiology report generation from imaging findings.
organoid-drug-response-agent	Analyze drug response in patient-derived organoids for personalized therapy prediction.
pdx-model-analysis-agent	Patient-derived xenograft model analysis for drug efficacy and biomarker discovery.
deep-visual-proteomics-agent	Deep visual proteomics: spatial proteomic analysis from laser-capture microdissection MS data.
exosome-ev-analysis-agent	Extracellular vesicle and exosome analysis: cargo profiling and biomarker discovery.
microbiome-cancer-agent	Tumor microbiome analysis and its role in cancer progression and immunotherapy response.
bio-fragment-analysis	Analyze cfDNA fragment size distributions and fragmentomics features (FinaleToolkit/Griffin) for cancer detection and tissue-of-origin assessment.

Hematology & Blood Disorders (BioOS)

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Skill	Description
myeloma-mrd-agent	Multiple myeloma MRD assessment from flow cytometry and NGS data.
mpn-progression-monitor-agent	Myeloproliferative neoplasm progression monitoring from serial molecular data.
mpn-research-assistant	Research assistant for myeloproliferative neoplasms: literature, mutation analysis, treatment.
bone-marrow-ai-agent	Bone marrow analysis: blast counting, immunophenotyping, disease classification.
hemoglobinopathy-analysis-agent	Hemoglobin variant analysis, sickle cell, and thalassemia genotype-phenotype assessment.
chip-clonal-hematopoiesis-agent	Clonal hematopoiesis of indeterminate potential (CHIP) variant detection and risk assessment.
coagulation-thrombosis-agent	Coagulation pathway analysis, thrombophilia assessment, anticoagulation guidance.

Immunology & Cell Therapy (BioOS)

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Skill	Description
cart-design-optimizer-agent	Optimize CAR-T cell construct design: scFv selection, linker, co-stimulatory domain.
armored-cart-design-agent	Design armored CAR-T cells with cytokine payloads and resistance mechanisms.
tcell-exhaustion-analysis-agent	Analyze T cell exhaustion from scRNA-seq and ATAC-seq data.
nk-cell-therapy-agent	NK cell therapy design: receptor engineering, expansion protocols, persistence.
tcr-pmhc-prediction-agent	Predict TCR-pMHC binding affinity and selectivity for TCR therapy design.
tcr-repertoire-analysis-agent	TCR repertoire analysis: V(D)J usage, clonotype dynamics, antigen specificity.
immune-checkpoint-combination-agent	Predict optimal immune checkpoint combination strategies from tumor immune microenvironment.
tme-immune-profiling-agent	Tumor microenvironment immune profiling: cell type deconvolution and spatial mapping.
cytokine-storm-analysis-agent	Cytokine storm detection, severity scoring, and intervention modeling.

Single-Cell & Spatial Agents (BioOS)

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Skill	Description
cellagent-annotation	AI-driven single-cell cluster annotation using marker gene databases.
universal-single-cell-annotator	Universal scRNA-seq annotator using foundation models and multi-reference integration.
scfoundation-model-agent	Single-cell foundation model inference (scFoundation/scGPT) for zero-shot annotation.
rna-velocity-agent	RNA velocity analysis with scVelo for trajectory and fate decision inference.
spatial-transcriptomics-agent	End-to-end spatial transcriptomics analysis: QC, deconvolution, domain detection.
spatial-transcriptomics-analysis	Spatial transcriptomics analysis with Squidpy and SpatialDE.
spatial-agent	Spatial omics agent: integrate spatial data with imaging, protein, and genomic layers.
nicheformer-spatial-agent	Spatial niche analysis with Nicheformer foundation model for tissue microenvironment.
spatial-epigenomics-agent	Spatial epigenomics analysis: spatially resolved chromatin accessibility and gene regulation.
bioinformatics-singlecell	General single-cell bioinformatics: clustering, trajectory, cell communication.
scrna-qc	Single-cell RNA-seq quality control: doublet removal, ambient RNA, filtering thresholds.
compbioagent-explorer	Computational biology exploration agent for multi-omics dataset analysis.
simo-multiomics-integration-agent	Single-cell multi-omics integration with SIMO/MOFA+ for joint embedding.
epigenomics-methylgpt-agent	Epigenomics and DNA methylation analysis with MethylGPT-inspired approaches.
biomaster-workflows	BioMaster workflow orchestration for end-to-end bioinformatics analyses.

Drug Discovery & Design (BioOS)

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Skill	Description
agentd-drug-discovery	AgentD autonomous drug discovery: target identification, hit finding, ADMET optimization.
chematagent-drug-discovery	CheMatAgent: chemistry-aware drug design with retrosynthesis and property optimization.
chemcrow-drug-discovery	ChemCrow drug discovery toolkit: web search, Python, chemical tools integration.
medea-therapeutic-discovery	MEDEA therapeutic discovery: multimodal evidence aggregation for target-disease validation.
molecule-evolution-agent	Directed molecular evolution: generative models for compound optimization and library design.
molecular-glue-discovery-agent	Molecular glue discovery: induced proximity degraders and ternary complex stabilizers.
protac-design-agent	PROTAC design: E3 ligase ligand selection, linker optimization, ternary complex modeling.
tpd-ternary-complex-agent	Targeted protein degradation ternary complex modeling and cooperativity prediction.
mage-antibody-generator	MAGE antibody generator: sequence design, humanization, affinity maturation.
antibody-design-agent	Antibody design: epitope mapping, CDR engineering, bispecific construction.
aav-vector-design-agent	AAV vector design: capsid selection, promoter optimization, payload capacity.
protein-structure-prediction	Protein structure prediction with AlphaFold3, ESMFold, or Boltz with comparison.
crispr-guide-design	CRISPR guide RNA design with on-target scoring and off-target minimization.
crispr-offtarget-predictor	Predict CRISPR Cas9/Cas12 off-target sites genome-wide with CRISPOR/Cas-OFFinder.
chemical-property-lookup	Look up chemical properties from PubChem, ChEMBL, DrugBank by name/SMILES.
chemistry-agent	General chemistry agent for synthesis planning, reaction prediction, and property calculation.
cryoem-ai-drug-design-agent	AI-guided drug design from cryo-EM structures: binding site analysis and docking.
time-resolved-cryoem-agent	Time-resolved cryo-EM analysis for dynamic structural biology.
cnv-caller-agent	Specialized CNV detection agent integrating multiple callers with ensemble scoring.
popeve-variant-predictor-agent	Variant pathogenicity prediction using EVE population-based evolutionary models.
varcadd-pathogenicity	VARCADD pathogenicity scoring for coding variants from structure and evolution.
variant-interpretation-acmg	ACMG/AMP variant interpretation with evidence-based classification framework.
gene-panel-design-agent	Design targeted gene panels for clinical or research sequencing applications.
pharmacogenomics-agent	Pharmacogenomics analysis: variant-drug interaction prediction and dosing recommendations.
multi-ancestry-prs-agent	Multi-ancestry polygenic risk score computation with ancestry-specific weighting.
prs-net-deep-learning-agent	Deep learning PRS prediction with PRSnet for complex traits.
cellfree-rna-agent	Cell-free RNA analysis: plasma cfRNA profiling for liquid biopsy diagnostics.
long-read-sequencing-agent	Long-read sequencing analysis: SV calling, methylation, isoform discovery, assembly.
bayesian-optimizer	Bayesian optimization for experimental design and hyperparameter tuning in biomedical research.

Clinical AI & Healthcare (BioOS)

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Skill	Description
chatehr-clinician-assistant	EHR clinical assistant: note summarization, structured data extraction, clinical decision support.
clinical-note-summarization	Summarize clinical notes into structured SOAP format with key findings.
clinical-nlp-extractor	Extract clinical entities (diagnoses, medications, procedures) from unstructured text.
ehr-fhir-integration	EHR-FHIR integration: HL7 FHIR resource creation, querying, and workflow automation.
fhir-development	FHIR API development: build SMART on FHIR apps and FHIR resource endpoints.
digital-twin-clinical-agent	Create patient digital twins for treatment simulation and outcome prediction.
trial-eligibility-agent	Assess patient eligibility for clinical trials from EHR data and trial criteria.
trialgpt-matching	TrialGPT patient-to-trial matching with eligibility assessment from clinical notes.
wearable-analysis-agent	Analyze wearable sensor data: activity, sleep, HRV, ECG for health monitoring.
multimodal-medical-imaging	Multimodal medical imaging analysis: CT, MRI, PET fusion and segmentation.
prior-auth-coworker	Prior authorization workflow assistant for insurance approval processes.
care-coordination	Care coordination agent: multi-disciplinary team communication and care plan management.
claims-appeals	Insurance claims appeals: documentation preparation and denial reasoning analysis.
lab-results	Lab result interpretation: reference ranges, trend analysis, critical value alerts.
drug-interaction-checker	Check drug-drug interactions from patient medication lists with severity scoring.
regulatory-drafter	Draft regulatory submissions: FDA, EMA, ICH document preparation.
regulatory-drafting	Regulatory writing and document structuring for medical device/drug submissions.
biomedical-data-analysis	Comprehensive biomedical data analysis: statistics, visualization, and interpretation.
data-visualization-biomedical	Biomedical-specific data visualization: clinical trial plots, survival curves, forest plots.

Research Infrastructure & Agents (BioOS)

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Skill	Description
biomni-general-agent	BioMni general biomedical agent for flexible multi-step research tasks.
biomni-research-agent	BioMni research-focused agent with literature, database, and analysis integration.
biokernel	BioKernel: unified computational kernel for bioinformatics tool orchestration.
biomcp-server	BioMCP: Model Context Protocol server for bioinformatics tool access.
mcpmed-bioinformatics-server	MCP server providing medical bioinformatics tool access to agents.
kragen-knowledge-graph	KRAGEN knowledge graph for biomedical entity relationships and reasoning.
leads-literature-mining	LEADS literature mining: automated extraction of biological findings from papers.
knowledge-synthesis	Synthesize knowledge from multiple biomedical sources into structured summaries.
deep-research-swarm	Multi-agent swarm for deep scientific research with parallel literature synthesis.
research-literature	Research literature management: search, organize, and synthesize scientific papers.
search-strategy	Design systematic search strategies for scientific literature and databases.
scientific-manuscript	Scientific manuscript writing and revision with journal-specific formatting.
cellular-senescence-agent	Cellular senescence analysis: marker scoring, SASP profiling, tissue aging assessment.
ngs-analysis	Next-generation sequencing data analysis orchestration and QC.
opentrons-protocol-agent	Opentrons liquid handler protocol design for automated lab workflows.
virtual-lab-agent	Virtual lab agent for in silico experiment simulation and protocol optimization.
data-visualization-expert	Expert data visualization for complex scientific and clinical datasets.
lobster-bioinformatics	Run bioinformatics analyses via Lobster AI: scRNA-seq, bulk RNA-seq, literature mining, dataset discovery, QC, and visualization.

📊 Data Science & Tools

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Statistics & Data Analysis

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Skill	Description
statistical-analysis	Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting.
statsmodels	Statistical modeling: OLS, GLM, logistic, ARIMA, time series, hypothesis tests, diagnostics, AIC/BIC, for rigorous statistical inference.
pymc	Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming.
simpy	Process-based discrete-event simulation for clinical systems: queues, resources, time-based events. Useful for modeling hospital workflows and patient flow.
exploratory-data-analysis	Comprehensive exploratory data analysis on scientific data files across 200+ file formats — structure, content, quality assessment, and visualization.
data-stats-analysis	Statistical tests, hypothesis testing, correlation analysis, and multiple testing corrections using scipy and statsmodels (OmicVerse).
data-transform	Transform, clean, reshape, and preprocess biological data using pandas and numpy (OmicVerse).
data-viz-plots	Create publication-quality plots and visualizations using matplotlib and seaborn (OmicVerse).
scientific-visualization	Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, PDF/EPS/TIFF export.

Lab Automation & Integration

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Skill	Description
opentrons-integration	Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management.
pylabrobot	Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment.
benchling-integration	Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, for lab data management automation.
labarchive-integration	Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap.
protocolsio-integration	Integration with protocols.io API for managing scientific protocols — search, create, update, publish protocols, and manage protocol steps and reagents.
instrument-data-to-allotrope	Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format for LIMS systems, data lakes, and downstream analysis.

Scientific Research & Writing

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Skill	Description
scientific-writing	Write scientific manuscripts in full paragraphs using a two-stage process: section outlines then full text. Covers all sections of research papers.
scientific-critical-thinking	Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB).
scientific-brainstorming	Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps.
hypothesis-generation	Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms.
scientific-problem-selection	Help scientists with research problem selection, project ideation, troubleshooting stuck projects, and strategic scientific decisions.
peer-review	Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review.
citation-management	Comprehensive citation management. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, generate BibTeX entries.
research-grants	Write competitive research proposals for NSF, NIH, DOE, and DARPA. Agency-specific formatting, review criteria, budget preparation, broader impacts.
research-lookup	Look up current research using Perplexity's Sonar Pro Search or Sonar Reasoning Pro via OpenRouter. Automatically selects best model for the query complexity.
biomni	Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis.
treatment-plans	Generate concise (3-4 page) medical treatment plans in LaTeX/PDF format for all clinical specialties including general medicine, rehabilitation, mental health, and chronic disease.

Analyst Personas

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Skill	Description
biologist-analyst	Expert biologist analyst persona for interpreting biological experiments, sequencing data, cell biology assays, and molecular biology research.
chemist-analyst	Expert chemist analyst persona for interpreting chemical data, synthesis routes, spectroscopic results, reaction mechanisms, and laboratory analyses.
epidemiologist-analyst	Expert epidemiologist analyst persona for study design, cohort analysis, risk factor assessment, public health surveillance, and causal inference.
psychologist-analyst	Expert psychologist analyst persona for behavioral data analysis, psychological assessment interpretation, clinical case formulation, and mental health research.

Public Health & Time Series

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Skill	Description
datacommons-client	Access public health statistics from Google Data Commons: disease prevalence, demographic data, health indicators across global sources.
timesfm-forecasting	Zero-shot time series forecasting with Google's TimesFM. For vital sign trends, health sensor data, and longitudinal health monitoring without custom model training.
aeon	Time series ML: classification, regression, clustering, anomaly detection, segmentation for temporal health data and sequential clinical measurements.

Scientific Literature & Reference Management

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Skill	Description
bgpt-paper-search	Search scientific papers with BGPT MCP server. Returns 25+ structured fields per paper: methods, results, sample sizes, quality scores. For literature reviews and evidence synthesis.
pyzotero	Interact with Zotero reference libraries programmatically via Zotero Web API v3. Retrieve, create, update items, export citations, upload PDFs, and build research automation workflows.
open-notebook	Self-hosted NotebookLM alternative. Ingest PDFs, videos, web pages, documents; generate AI-powered notes; chat with research materials; supports 16+ AI providers.

Data Processing & Scientific Computing

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Skill	Description
dask	Distributed computing for larger-than-RAM genomics/omics datasets. Scale pandas/NumPy beyond memory, parallel file processing, distributed ML.
polars	Fast in-memory DataFrame library (1-100GB). Faster pandas replacement for biomedical data ETL and analysis pipelines.
vaex	Out-of-core DataFrame operations for billions of rows. Fast statistics and visualization for large genomic and clinical datasets.
zarr-python	Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration for large-scale omics data.
pytorch-lightning	Organized PyTorch deep learning for biomedical AI: multi-GPU training, callbacks, logging, distributed training for clinical/genomic models.

Scientific Visualization & Communication

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Skill	Description
matplotlib	Low-level plotting library for full customization. Publication-quality figures for scientific manuscripts and journals.
seaborn	Statistical visualization with pandas integration. Box plots, violin plots, heatmaps, pair plots for biomedical data exploration.
plotly	Interactive visualization. Hover info, zoom, dashboards for exploratory biomedical analysis and presentations.
infographics	Create professional scientific infographics with iterative AI refinement. Supports 10 infographic types and 8 industry styles.
scientific-schematics	Publication-quality scientific diagrams: neural network architectures, biological pathways, system diagrams, flowcharts.
scientific-slides	Build research presentation slide decks for conferences, seminars, thesis defenses. PowerPoint and LaTeX Beamer support.
latex-posters	Create professional research posters in LaTeX (beamerposter, tikzposter). Conference posters with multi-column layouts.
pptx-posters	HTML/CSS research posters exportable to PDF or PPTX. Modern web-based poster design.
markdown-mermaid-writing	Scientific documentation with Markdown and 24 Mermaid diagram types. 9 document templates for scientific reports.
paper-2-web	Convert academic papers to interactive websites, presentation videos, and conference posters (Paper2Web, Paper2Video, Paper2Poster).

Additional Scientific Tools

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Skill	Description
pymoo	Multi-objective optimization with PYMOO. Drug design parameter optimization, Pareto front analysis, evolutionary algorithms.
markitdown	Convert documents (PDF, DOCX, PPTX, HTML, images) to Markdown for processing and analysis.
perplexity-search	AI-powered search via Perplexity for real-time scientific information retrieval.
geopandas	Geospatial data analysis with GeoPandas. Epidemiology mapping, disease distribution, spatial health analytics.
hypogenic	Automated hypothesis generation and testing on tabular datasets. Combine literature insights with data-driven hypothesis validation.
pdf-processing	Advanced PDF processing: text extraction, table parsing, annotation, form filling.
pdf-processing-pro	Professional PDF processing with enhanced OCR, multi-column layout handling, and batch processing.
pdf-anthropic	Anthropic-optimized PDF analysis for scientific and medical document comprehension.
xlsx-official	Official Excel/XLSX skill for spreadsheet creation, analysis, and data management.
docx-official	Official Word/DOCX skill for document creation, editing, and formatting.
pptx-official	Official PowerPoint/PPTX skill for presentation creation and editing.

Computational Simulation & Ontology (HeshamFS/materials-simulation-skills)

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Skill	Description
ontology-validator	Validate biomedical ontology structures and term relationships (HPO, GO, MeSH, SNOMED, OBO).
ontology-explorer	Navigate and query biomedical ontologies: term hierarchies, annotations, cross-references.
ontology-mapper	Map between biomedical ontologies: HPO↔OMIM, GO↔UniProt, disease↔phenotype cross-ontology.
slurm-job-script-generator	Generate SLURM sbatch scripts for HPC genomics/bioinformatics pipeline jobs with optimized resource requests.
numerical-integration	Select and configure ODE/PDE time integration for biological model simulation (stiff systems, IMEX).
nonlinear-solvers	Configure nonlinear solvers for biological network optimization, parameter fitting, FBA.
parameter-optimization	Design of experiments, sensitivity analysis, Bayesian optimization for biological model calibration.
linear-solvers	Select linear solvers for large-scale biological network and metabolic model computations.
numerical-stability	Analyze numerical stability for time-dependent biological simulations (CFL criteria, stiffness).
simulation-orchestrator	Orchestrate multi-simulation campaigns: parameter sweeps, batch jobs, result aggregation.
simulation-validator	Validate simulations: pre-flight checks, runtime monitoring, convergence, NaN/Inf detection.
convergence-study	Spatial/temporal convergence analysis with Richardson extrapolation for simulation verification.
post-processing	Extract, analyze, and visualize simulation output data: time series, field profiles, statistics.
performance-profiling	Identify computational bottlenecks, analyze scaling behavior, optimize HPC simulation jobs.
differentiation-schemes	Select finite difference/volume/spectral schemes for PDE discretization in biological models.
time-stepping	Adaptive time-step control for biological dynamics: CFL constraints, checkpoint scheduling.
mesh-generation	Mesh generation for numerical simulations: resolution, quality metrics, adaptive refinement.

Developer Workflow Skills (obra/superpowers)

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Skill	Description
test-driven-development	TDD workflow: write tests before implementation, red-green-refactor cycle for reliable code.
systematic-debugging	Structured debugging approach: hypothesis formation, evidence gathering, root cause analysis.
dispatching-parallel-agents	Orchestrate parallel subagents for independent tasks to maximize throughput.
writing-plans	Write structured implementation plans before touching code for complex multi-step tasks.
executing-plans	Execute written implementation plans with review checkpoints in isolated sessions.
brainstorming	Structured creative exploration of requirements and design before implementation.
writing-skills	Create and verify new SKILL.md skills with proper format and deployment validation.
verification-before-completion	Run verification commands and confirm outputs before claiming work is complete.
requesting-code-review	Structure code review requests with context, changes summary, and specific questions.
receiving-code-review	Process code review feedback with technical rigor rather than blind acceptance.
subagent-driven-development	Break development tasks into subtasks for parallel subagent execution.
using-git-worktrees	Create isolated git worktrees for feature work and plan execution.
finishing-a-development-branch	Complete development branches: merge, PR, or cleanup with structured decision options.
using-superpowers	Meta-skill: discover and use available skills for any task at conversation start.

Acknowledgements

We have benefited from the following excellent projects. If you’re interested, please check them out.

OpenClaw Medical Skills

What Is This?

Why This Collection Matters

Installation

Requirements

For OpenClaw Users

Method 1 — Clone and Copy (Recommended)

Method 2 — OpenClaw CLI

Method 3 — Configure Extra Directories

Method 4 — Install Selected Skills Only

For NanoClaw Users

Verification

Skills Overview

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

General Tools

🏥 Medical & Clinical

Medical Tools

Drug Safety & Chemical Biology

Medical Imaging & Pathology

Healthcare ML & Clinical AI

Health & Wellness Analytics

Mental Health & Crisis Intervention

Medical Device & Regulatory

🗂️ Scientific Databases

Scientific Databases (Genomics & Variants)

Scientific Databases (Proteins, Pathways & Drugs)

Cancer Genomics Databases

Genomic & Molecular Databases

Structural Biology & Drug Discovery

🧬 Bioinformatics (gptomics bio-* suite)

Bioinformatics Tools & Pipelines

Bioinformatics — Clinical Databases & Variant Analysis

Bioinformatics — Sequencing & Read QC

Bioinformatics — Differential Expression & Transcriptomics

Bioinformatics — Pathway & Network Analysis

Bioinformatics — Single-Cell & Spatial Omics

Bioinformatics — Epigenomics & Chromatin

Bioinformatics — Metagenomics & Microbiome

Bioinformatics — Immunoinformatics & Flow Cytometry

Bioinformatics — Multi-Omics Integration

Bioinformatics — Proteomics & Metabolomics

Bioinformatics — Structural Biology & Cheminformatics

Bioinformatics — Epidemiological & Causal Genomics

🔬 Omics & Computational Biology

Single-Cell & Spatial Omics

Cheminformatics & Drug Discovery

Proteomics & Mass Spectrometry

Protein Structure & Design

Single-Cell & Trajectory Analysis

Phylogenetics & Network Analysis

⚙️ ClawBio Pipelines

Bioinformatics Orchestration & Pipelines (ClawBio)

Genomics, Ancestry & Pharmacogenomics (ClawBio)

Structural Biology & Literature (ClawBio)

🧠 BioOS Extended Suite

BioOS Extended Bioinformatics Suite (mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-)

Sequence & Alignment Tools

Sequence Analysis

Read Alignment

Genome Assembly

Genome Intervals & Annotation

RNA Quantification

Epitranscriptomics & CLIP-seq

Small RNA-seq

Population Genetics & Phasing

Comparative Genomics & Phylogenetics

Systems Biology & Metabolic Modeling

Experimental Design & Reporting

End-to-End Workflow Pipelines

Data Visualization (Bioinformatics)