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.
geopandas
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
get-available-resources
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
gget
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
gh-address-comments
Help address review/issue comments on the open GitHub PR for the current branch using gh CLI; verify gh auth first and prompt the user to authenticate if not logged in.
gh-fix-ci
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.
gtars
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.
gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
histolab
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
hmdb-database
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
hypogenic
Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research discovery in domains like deception detection, AI content detection, mental health analysis, or other empirical research tasks.
hypothesis-generation
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
it-operations
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-pr
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.
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
lamindb
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.
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
latex-posters
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.
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.).
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.
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.
matchms
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
matplotlib
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
complexity-analyzer
Measure and report code complexity metrics with actionable recommendations.
spawn-parallel
Pattern for spawning parallel subagents efficiently. Use when you need multiple independent tasks done concurrently.
verify-output
Pattern for verifying your output matches required schema before completing. Use before writing final output to ensure validity.
wrangler
Cloudflare Workers CLI for deploying, developing, and managing Workers, KV, R2, D1, Vectorize, Hyperdrive, Workers AI, Containers, Queues, Workflows, Pipelines, and Secrets Store. Load before running wrangler commands to ensure correct syntax and best practices.
architecture-diagram
Create professional, dark-themed architecture diagrams as standalone HTML files with SVG graphics. Use when the user asks for system architecture diagrams, infrastructure diagrams, cloud architecture visualizations, security diagrams, network topology diagrams, or any technical diagram showing system components and their relationships.
calculator
Performs arbitrary-precision arithmetic calculations including addition, subtraction, multiplication, division, and exponents. Use when the user asks to calculate, compute, or evaluate math expressions, or when precise decimal arithmetic is needed to avoid floating-point errors.
jira-cli
Interact with Jira from the command line to create, list, view, edit, and transition issues, manage sprints and epics, and perform common Jira workflows. Use when the user asks about Jira tasks, tickets, issues, sprints, or needs to manage project work items.
release
Create a new version release with git tag and GitHub Release. Use when user asks to release, publish, create a new version, or ship a release. (project)
autofix
Auto-fix CodeRabbit review comments - get CodeRabbit review comments from GitHub and fix them interactively or in batch
dispatching-parallel-agents
Dispatches one subagent per independent domain to parallelize investigation/fixes. Use when you have 2+ unrelated failures (e.g., separate failing test files, subsystems, bugs) with no shared state or ordering dependencies.
executing-plans
Disciplined plan execution for implementation tasks. Use when executing a saved implementation plan, following step-by-step instructions from a plan document.
finishing-a-development-branch
Git branch completion workflow. Use when implementation is complete, tests pass, and a feature branch needs to be integrated via merge, pull request, or cleanup.
receiving-code-review
Assesses and responds to incoming code review feedback on PRs (reviewer comments, requested changes), especially when suggestions are unclear, technically questionable, or scope-expanding. Use before implementing review suggestions to align on intent and keep changes minimal.
requesting-code-review
Use when you need to request a code review for a PR/MR and want a consistent review brief (context, scope, risk areas, test instructions, acceptance criteria) before merge.
subagent-driven-development
Sequential subagent execution with two-stage review gates for implementation plans. Use when executing multi-task plans in current session, when tasks need fresh subagent context to avoid pollution, when formal review cycles (spec compliance then code quality) are required between tasks, or when you need diff-based validation of each task before proceeding.
test-driven-development
Red-green-refactor development methodology requiring verified test coverage. Use for feature implementation, bugfixes, refactoring, or any behavior changes where tests must prove correctness.
using-git-worktrees
Git worktree–based workspace isolation for parallel or non-disruptive development. Use when work must occur without modifying or interfering with the current working tree.
using-superpowers
Meta-skill enforcing skill discovery and invocation discipline through mandatory workflows. Use when starting any conversation to check for relevant skills before any response, ensuring skill-first workflow before proceeding.
writing-plans
Structured implementation planning for multi-step development tasks. Use when you have a spec or requirements and need to break work into executable steps.
writing-skills
Use when creating new skills, editing existing skills, or verifying skills work before deployment
marimo-development
Expert guidance for creating and working with marimo notebooks - reactive Python notebooks that can be executed as scripts and deployed as apps. Use when the user asks to create marimo notebooks, convert Jupyter notebooks to marimo, build interactive dashboards or data apps with marimo, work with marimo's reactive programming model, debug marimo notebooks, or needs help with marimo-specific features (cells, UI elements, reactivity, SQL integration, deploying apps, etc.).
pixi-package-manager
Fast, reproducible scientific Python environments with pixi - conda and PyPI unified
python-style-guide
Comprehensive Python programming guidelines based on Google's Python Style Guide. Use when Claude needs to write Python code, review Python code for style issues, refactor Python code, or provide Python programming guidance. Covers language rules (imports, exceptions, type annotations), style rules (naming conventions, formatting, docstrings), and best practices for clean, maintainable Python code.
r-development
Modern R development practices emphasizing tidyverse patterns (dplyr 1.1 and later, native pipe, join_by, .by grouping), rlang metaprogramming, performance optimization, and package development. Use when Claude needs to write R code, create R packages, optimize R performance, or provide R programming guidance.
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