Claude Skills
The open format is called Agent Skills and works in Claude Code, Codex, Cursor and other agents — most people know it as Claude Skills.
Every Agent Skill we could find on GitHub, deduplicated by content. 86 696 files from 2 113 authors, of which 68 413 are unique — the rest is the same skill repackaged into someone else's repository. For each one: what it weighs in tokens, whether it ships runnable scripts, and which MCP servers it needs.
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
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.
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).
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.
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
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.
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Perform code reviews following Sentry engineering practices. Use when reviewing pull requests, examining code changes, or providing feedback on code quality. Covers security, performance, testing, and design review.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Create a concise plan. Use when a user explicitly asks for a plan related to a coding task.
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.
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.
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
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.
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.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
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.
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
Find bugs, security vulnerabilities, and code quality issues in local branch changes. Use when asked to review changes, find bugs, security review, or audit code on the current branch.
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.
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
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.
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
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.
Inspect GitHub PR checks with gh, pull failing GitHub Actions logs, summarize failure context, then create a fix plan and implement after user approval. Use when a user asks to debug or fix failing PR CI/CD checks on GitHub Actions and wants a plan + code changes; for external checks (e.g., Buildkite), only report the details URL and mark them out of scope.
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
Manages IT infrastructure, monitoring, incident response, and service reliability. Provides frameworks for ITIL service management, observability strategies, automation, backup/recovery, capacity planning, and operational excellence practices.
Iterate on a PR until CI passes. Use when you need to fix CI failures, address review feedback, or continuously push fixes until all checks are green. Automates the feedback-fix-push-wait cycle.
Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
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.).
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.
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.
Analyzes Move language packages against the official Move Book Code Quality Checklist. Use this skill when reviewing Move code, checking Move 2024 Edition compliance, or analyzing Move packages for best practices. Activates automatically when working with .move files or Move.toml manifests.
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.
Capture conversations and decisions into structured Notion pages; use when turning chats/notes into wiki entries, how-tos, decisions, or FAQs with proper linking.
Turn Notion specs into implementation plans, tasks, and progress tracking; use when implementing PRDs/feature specs and creating Notion plans + tasks from them.
This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.
Extract text and tables from PDF files, fill forms, merge documents. Use when working with PDF files or when the user mentions PDFs, forms, or document extraction.
Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.
This skill should be used when the user asks about "plugin settings", "store plugin configuration", "user-configurable plugin", ".local.md files", "plugin state files", "read YAML frontmatter", "per-project plugin settings", or wants to make plugin behavior configurable. Documents the .claude/plugin-name.local.md pattern for storing plugin-specific configuration with YAML frontmatter and markdown content.
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
Guides security professionals in implementing defense-in-depth security architectures, achieving compliance with industry frameworks (SOC2, ISO27001, GDPR, HIPAA), conducting threat modeling and risk assessments, managing security operations and incident response, and embedding security throughout the SDLC.
Search Engine Optimization specialist for content strategy, technical SEO, keyword research, and ranking improvements. Use when optimizing website content, improving search rankings, conducting keyword analysis, or implementing SEO best practices. Expert in on-page SEO, meta tags, schema markup, and Core Web Vitals.
This skill should be used when the user wants to "create a skill", "add a skill to plugin", "write a new skill", "improve skill description", "organize skill content", or needs guidance on skill structure, progressive disclosure, or skill development best practices for Claude Code plugins.
Install Codex skills into $CODEX_HOME/skills from a curated list or a GitHub repo path. Use when a user asks to list installable skills, install a curated skill, or install a skill from another repo (including private repos).
Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability.
Reference for all AI tools available in DBX Studio's AI chat system. Use when adding, modifying, or debugging AI tool definitions, tool execution, or provider integrations.
Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.
Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.
Chart and visualization generation for DBX Studio. Use when a user wants to visualize data — bar charts, line graphs, pie charts, scatter plots, etc.
Claude Skills — questions
Answers built from the skills we actually parsed.