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. 79 341 files from 1 736 authors, of which 61 700 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.
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. Best for proteomics, comprehensive MS data processing. For simple spectral comparison and metabolite ID use matchms.
Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+ services). Use this for direct HTTP/REST work or UniProt-specific control.
Use this skill for processing and analyzing large tabular datasets (billions of rows) that exceed available RAM. Vaex excels at out-of-core DataFrame operations, lazy evaluation, fast aggregations, efficient visualization of big data, and machine learning on large datasets. Apply when users need to work with large CSV/HDF5/Arrow/Parquet files, perform fast statistics on massive datasets, create visualizations of big data, or build ML pipelines that do not fit in memory.
Google quantum computing framework. Use when targeting Google Quantum AI hardware, designing noise-aware circuits, or running quantum characterization experiments. Best for Google hardware, noise modeling, and low-level circuit design. For IBM hardware use qiskit; for quantum ML with autodiff use pennylane; for physics simulations use qutip.
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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.
Comprehensive toolkit for preparing ISO 13485 certification documentation for medical device Quality Management Systems. Use when users need help with ISO 13485 QMS documentation, including (1) conducting gap analysis of existing documentation, (2) creating Quality Manuals, (3) developing required procedures and work instructions, (4) preparing Medical Device Files, (5) understanding ISO 13485 requirements, or (6) identifying missing documentation for medical device certification. Also use when users mention medical device regulations, QMS certification, FDA QMSR, EU MDR, or need help with quality system documentation.
Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.
Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service operations, network traffic, logistics, or any system where entities interact with shared resources over time.
Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.
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.
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.
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.
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing information beyond the model knowledge cutoff. Provides access to multiple Perplexity models including Sonar Pro, Sonar Pro Search (advanced agentic search), and Sonar Reasoning Pro through a single OpenRouter API key.
Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.
Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
Chunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
Interact with Zotero reference management libraries using the pyzotero Python client. Retrieve, create, update, and delete items, collections, tags, and attachments via the Zotero Web API v3. Use this skill when working with Zotero libraries programmatically, managing bibliographic references, exporting citations, searching library contents, uploading PDF attachments, or building research automation workflows that integrate with Zotero.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quantum error mitigation, and enterprise quantum computing. For Google hardware use cirq; for gradient-based quantum ML use pennylane; for open quantum system simulations use qutip.
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.
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.
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.
Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures use matplotlib or scientific-visualization.
Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
Vue Router 4 patterns, navigation guards, route params, and route-component lifecycle interactions.
Use for Vue.js testing. Covers Vitest, Vue Test Utils, component testing, mocking, testing patterns, and Playwright for E2E testing.
> Audit every endpoint in a PostHog project for staleness, failed materialisations, and unused materialised versions. Use when the user asks "what endpoints can I clean up?", "are any of my endpoints broken?", "which materialised versions are still being called?", or wants a one-shot cleanup pass over the Endpoints product. Produces a prioritised report grouped by issue type, with recommended actions but does not modify anything without explicit confirmation.
Audit PostHog experiments and feature flags for configuration issues, staleness, and best-practice violations. Read when the user asks to audit, health-check, or review experiments or feature flags, check flag hygiene, or verify experiment setup.
Analyze session replay patterns across experiment variants to understand user behavior differences. Use when the user wants to see how users interact with different experiment variants, identify usability issues, compare behavior patterns between control and test groups, or get qualitative insights to complement quantitative experiment results.
Identify and clean up stale feature flags in a PostHog project. Use when the user wants to find unused, fully rolled out, or abandoned feature flags, review them for safety, and then disable or delete them. Covers staleness detection, dependency checking, and safe removal workflows.
Copy a feature flag from one PostHog project to one or more target projects in the same organization. Use when the user wants to duplicate a flag, promote a flag from staging to production, sync flags across projects, or replicate a flag configuration in a different workspace. Covers cohort remapping, scheduled-change handling, encrypted payloads, and the safe defaults (disabled in target, no scheduled changes).
> Create a recurring AI-generated PostHog report — schedule a free-text prompt to run on a cron, with the LLM-synthesized markdown delivered to email or Slack on each tick. Use when the user wants a recurring AI summary of X on any cadence (daily, weekly, monthly, yearly) rather than a one-off report. (To attach an AI summary to an existing insight/dashboard subscription instead of a free-text prompt, see `managing-subscriptions` and its `summary_enabled` option.)
> Create a PostHog endpoint with the right shape on the first try — covers query kind choice, name conventions, what to expose as variables (HogQL code_name vs insight breakdown), data_freshness_seconds, and whether to materialise on day one. Use when the user says "create an endpoint", "expose this query as an API", "turn this insight into an endpoint", or asks for help structuring a new compare mode, inline-only variables on a materialised endpoint, unbounded date ranges, ambiguous names.
> Debugs why session recordings aren't appearing in the local dev environment. Use when a developer reports that local replay ingestion isn't working, recordings aren't showing up despite /s calls, or the replay pipeline SDK capture, Caddy proxy, capture-replay (Rust), Kafka, ingestion-sessionreplay (Node), recording-api (Node), SeaweedFS, and common failure modes like orphaned processes, stuck phrocs workers, and trigger misconfiguration.
> Diagnoses why a session recording is missing or was not captured. Use when a user asks why a session has no replay, why recordings aren't appearing, or wants to troubleshoot session replay capture issues for a specific session ID or across their project. Covers SDK diagnostic signals, project settings, sampling, triggers, ad blockers, and quota/billing scenarios.
> Help users debug PostHog Error Tracking stack-trace symbolication for any supported platform — JavaScript/TypeScript web, React Native (Hermes), Android (Proguard / R8), or iOS / macOS (dSYM). The PostHog symbol-set lookup flow is universal across platforms; build-tool and artifact details live in per-platform references (JavaScript is fleshed out, others come as we encounter them). Use when stack frames stay minified or obfuscated after symbols are uploaded, PostHog symbol sets show last_used but frames are not readable, chunk IDs or dSYM UUIDs do not match, "Token not found" appears, uploaded source maps / dSYMs / Proguard mappings look empty, or bundler / symbol-upload configuration needs troubleshooting.
> Export PostHog events, persons, or sessions on demand and download the resulting files. Use when the user asks to download/export raw PostHog data, create a one-off file export, fetch a Parquet or JSONLines export, or use the file_download_batch_exports API. Covers starting the export with MCP, polling completion, and downloading via the existing REST redirect endpoint.
> Explore and diagnose a PostHog endpoint's execution logs — error messages, failed runs, cache misses, slow runs, or unexpected row counts during endpoint invocations. Use when the user says "my endpoint is failing", "show me the logs for endpoint X", "what error did endpoint Y produce", "why did endpoint Z return no rows", "is this endpoint hitting cache", or "check the last N runs". Focused on a single named endpoint's runtime log entries, not project-wide auditing or query performance profiling.
> Diagnoses the health of a project's PostHog SDK integrations — which SDKs are out of date and how to fix them. Use when a user asks about PostHog SDK versions, outdated SDKs, upgrade recommendations, "SDK health", "SDK doctor" (the former name), or when events or features seem off and it might be due to an old SDK.
Inspects PostHog Web analytics Live tab data — current users online, last-30-minutes pageviews, top pages, referrers, devices, browsers, countries, bot traffic, and the per-minute bot/users charts. Use when the user asks "who is on my site right now?", "what is happening live?", "what bots are crawling me?", asks about the "live tab" / "live dashboard", wants live numbers (last 30 min), or wants help filtering or drilling into the live view. Also covers building product-analytics insights that mirror what the tiles show.
> ABSOLUTE MUST to debug and inspect LLM/AI agent traces using PostHog's MCP tools. Use when the user pastes a trace or session URL (e.g. /ai-observability/traces/<id> or /ai-observability/sessions/<id>), asks to debug a trace, figure out what went wrong, check if an agent used a tool correctly, verify context/files were surfaced, inspect subagent behavior, investigate LLM decisions, or analyze token usage and costs. Also use when raw SQL/HogQL against `events.properties.$ai_input` / `$ai_output_choices` returns empty — message content lives only on the dedicated `posthog.ai_events` table.
Claude Skills — questions
Answers built from the skills we actually parsed.