matchms
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
markitdown
Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
market-research-reports
Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, deep integration with research-lookup for data gathering, and multi-framework strategic analysis including Porter's Five Forces, PESTLE, SWOT, TAM/SAM/SOM, and BCG Matrix.
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
executing-marketing-campaigns
Plans, creates, and optimizes marketing campaigns including content strategy, social media, email, and analytics. Helps develop go-to-market strategies, campaign messaging, and performance measurement.
excel-analysis
Analyze Excel spreadsheets, create pivot tables, generate charts, and perform data analysis. Use when analyzing Excel files, spreadsheets, tabular data, or .xlsx files.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
error-resolver
Systematic error diagnosis and resolution using first-principle analysis. Use when encountering any error message, stack trace, or unexpected behavior. Supports replay functionality to record and reuse solutions.
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.
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. Supports multiple formats.
email-composer
Draft professional emails for various contexts including business, technical, and customer communication. Use when the user needs help writing emails or composing professional messages.
drugbank-database
Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
devops-iac-engineer
Implements infrastructure as code using Terraform, Kubernetes, and cloud platforms. Designs scalable architectures, CI/CD pipelines, and observability solutions. Provides security-first DevOps practices and site reliability engineering guidance.
deslop
Remove AI-generated code slop from a branch. Use when cleaning up AI-generated code, removing unnecessary comments, defensive checks, or type casts. Checks diff against main and fixes style inconsistencies.
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
datacommons-client
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
data-privacy-compliance
Data privacy and regulatory compliance specialist for GDPR, CCPA, HIPAA, and international data protection laws. Use when implementing privacy controls, conducting data protection impact assessments, ensuring regulatory compliance, or managing data subject rights. Expert in consent management, data minimization, and privacy-by-design principles.
dask
Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.
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.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
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.
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-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
citation-management
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
cirq
Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).
chembl-database
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
container-management
Create, manage, and optimize LXC containers in Proxmox. Control container lifecycle, manage resources, and coordinate container deployments across nodes.
cluster-management
Monitor and manage Proxmox cluster nodes, resources, and infrastructure health. Track node status, cluster quorum, and resource allocation across your virtualization platform.
snowtower-user
Helps end-users get Snowflake access and use the platform. Use when users ask about requesting access, generating RSA keys, connecting to Snowflake, or basic Snowflake usage. Triggers on mentions of access requests, RSA keys, connection issues, or "how do I get access".
snowtower-maintainer
Maintains SnowTower project documentation, README, and Claude configuration. Use when updating documentation, auditing .claude folder contents, syncing README with actual project state, or reviewing agent/pattern definitions. Triggers on mentions of documentation, README, maintenance, or .claude folder updates.
snowtower-admin
Advanced skill for SnowTower infrastructure administrators. Use for SnowDDL operations, user provisioning, role management, CI/CD deployments, troubleshooting, and Snowflake administration. Triggers on mentions of snowddl, deploy, user creation, role grants, infrastructure changes, or admin operations.
summon-daem0n
Guide for initializing and consolidating Daem0n-MCP across project structures
openspec-daem0n-bridge
Bridges OpenSpec (spec-driven development) with Daem0n-MCP memory - auto-imports specs, informs proposals with past outcomes, converts archived changes to learnings
gemini-research-subagent
Delegates large-context code analysis to Gemini CLI. Use when analyzing codebases, tracing bugs across files, reviewing architecture, or performing security audits. Gemini reads, Claude implements.
daem0nmcp-protocol
Use when Daem0nMCP tools are available - enforces the sacred covenant (commune at session start, seek counsel before changes, inscribe decisions, seal outcomes)
skool-money-model-strategist
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skills-factory
Meta-skill for creating production-ready Claude Code skills using evaluation-driven development, progressive disclosure patterns, comprehensive validation, and two-Claude iterative methodology
project-creator
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darkit-gin
基于 gin-gonic/gin 的企业级 Web 框架增强版，提供开箱即用的 JWT 认证、SSE 实时通信、缓存管理、OpenAPI 文档生成等企业级功能。涵盖选项式路由配置、统一响应格式、中间件管理、安全加固、性能优化等完整开发能力。
raindrop-io
Manage Raindrop.io bookmarks with AI assistance. Save and organize bookmarks, search your collection, manage reading lists, and organize research materials. Use when working with bookmarks, web research, reading lists, or when user mentions Raindrop.io.
testing-gate
Gate 6 - Verify tests exist and cover critical paths. Issues result in WARNINGS (encourages tests, doesn't block).
testing-fundamentals
Auto-invoke when reviewing test files or discussing testing strategy. Enforces testing pyramid, strategic coverage, and stack-appropriate frameworks.
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