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.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
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.
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.
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.
deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
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.
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.
etetoolkit
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
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.
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.
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.
testing-skills-with-subagents
Use when creating or editing skills, before deployment, to verify they work under pressure and resist rationalization - applies RED-GREEN-REFACTOR cycle to process documentation by running baseline without skill, writing to address failures, iterating to close loopholes
testing-anti-patterns
Use when writing or changing tests, adding mocks, or tempted to add test-only methods to production code - prevents testing mock behavior, production pollution with test-only methods, and mocking without understanding dependencies
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.
brainstorming
Use when creating or developing, before writing code or implementation plans - refines rough ideas into fully-formed designs through collaborative questioning, alternative exploration, and incremental validation. Don't use during clear 'mechanical' processes
condition-based-waiting
Use when tests have race conditions, timing dependencies, or inconsistent pass/fail behavior - replaces arbitrary timeouts with condition polling to wait for actual state changes, eliminating flaky tests from timing guesses
defense-in-depth
Use when invalid data causes failures deep in execution, requiring validation at multiple system layers - validates at every layer data passes through to make bugs structurally impossible
dispatching-parallel-agents
Use when facing 3+ independent failures that can be investigated without shared state or dependencies - dispatches multiple Claude agents to investigate and fix independent problems concurrently
test-driven-development
Use when implementing any feature or bugfix, before writing implementation code - write the test first, watch it fail, write minimal code to pass; ensures tests actually verify behavior by requiring failure first
executing-plans
Use when partner provides a complete implementation plan to execute in controlled batches with review checkpoints - loads plan, reviews critically, executes tasks in batches, reports for review between batches
finishing-a-development-branch
Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured options for merge, PR, or cleanup
receiving-code-review
Use when receiving code review feedback, before implementing suggestions, especially if feedback seems unclear or technically questionable - requires technical rigor and verification, not performative agreement or blind implementation
requesting-code-review
Use when completing tasks, implementing major features, or before merging to verify work meets requirements - dispatches superpowers:code-reviewer subagent to review implementation against plan or requirements before proceeding
sharing-skills
Use when you've developed a broadly useful skill and want to contribute it upstream via pull request - guides process of branching, committing, pushing, and creating PR to contribute skills back to upstream repository
subagent-driven-development
Use when executing implementation plans with independent tasks in the current session - dispatches fresh subagent for each task with code review between tasks, enabling fast iteration with quality gates
nodejs-backend-patterns
Build production-ready Node.js backend services with Express/Fastify, implementing middleware patterns, error handling, authentication, database integration, and API design best practices. Use when creating Node.js servers, REST APIs, GraphQL backends, or microservices architectures.
typescript-advanced-types
Master TypeScript's advanced type system including generics, conditional types, mapped types, template literals, and utility types for building type-safe applications. Use when implementing complex type logic, creating reusable type utilities, or ensuring compile-time type safety in TypeScript projects.
gitops-workflow
Implement GitOps workflows with ArgoCD and Flux for automated, declarative Kubernetes deployments with continuous reconciliation. Use when implementing GitOps practices, automating Kubernetes deployments, or setting up declarative infrastructure management.
helm-chart-scaffolding
Design, organize, and manage Helm charts for templating and packaging Kubernetes applications with reusable configurations. Use when creating Helm charts, packaging Kubernetes applications, or implementing templated deployments.
k8s-manifest-generator
Create production-ready Kubernetes manifests for Deployments, Services, ConfigMaps, and Secrets following best practices and security standards. Use when generating Kubernetes YAML manifests, creating K8s resources, or implementing production-grade Kubernetes configurations.
k8s-security-policies
Implement Kubernetes security policies including NetworkPolicy, PodSecurityPolicy, and RBAC for production-grade security. Use when securing Kubernetes clusters, implementing network isolation, or enforcing pod security standards.
langchain-architecture
Design LLM applications using the LangChain framework with agents, memory, and tool integration patterns. Use when building LangChain applications, implementing AI agents, or creating complex LLM workflows.
code-review-excellence
Master effective code review practices to provide constructive feedback, catch bugs early, and foster knowledge sharing while maintaining team morale. Use when reviewing pull requests, establishing review standards, or mentoring developers.
auth-implementation-patterns
Master authentication and authorization patterns including JWT, OAuth2, session management, and RBAC to build secure, scalable access control systems. Use when implementing auth systems, securing APIs, or debugging security issues.
terraform-module-library
Build reusable Terraform modules for AWS, Azure, and GCP infrastructure following infrastructure-as-code best practices. Use when creating infrastructure modules, standardizing cloud provisioning, or implementing reusable IaC components.
multi-cloud-architecture
Design multi-cloud architectures using a decision framework to select and integrate services across AWS, Azure, and GCP. Use when building multi-cloud systems, avoiding vendor lock-in, or leveraging best-of-breed services from multiple providers.
hybrid-cloud-networking
Configure secure, high-performance connectivity between on-premises infrastructure and cloud platforms using VPN and dedicated connections. Use when building hybrid cloud architectures, connecting data centers to cloud, or implementing secure cross-premises networking.
cost-optimization
Optimize cloud costs through resource rightsizing, tagging strategies, reserved instances, and spending analysis. Use when reducing cloud expenses, analyzing infrastructure costs, or implementing cost governance policies.
secrets-management
Implement secure secrets management for CI/CD pipelines using Vault, AWS Secrets Manager, or native platform solutions. Use when handling sensitive credentials, rotating secrets, or securing CI/CD environments.
gitlab-ci-patterns
Build GitLab CI/CD pipelines with multi-stage workflows, caching, and distributed runners for scalable automation. Use when implementing GitLab CI/CD, optimizing pipeline performance, or setting up automated testing and deployment.
github-actions-templates
Create production-ready GitHub Actions workflows for automated testing, building, and deploying applications. Use when setting up CI/CD with GitHub Actions, automating development workflows, or creating reusable workflow templates.
deployment-pipeline-design
Design multi-stage CI/CD pipelines with approval gates, security checks, and deployment orchestration. Use when architecting deployment workflows, setting up continuous delivery, or implementing GitOps practices.
web3-testing
Test smart contracts comprehensively using Hardhat and Foundry with unit tests, integration tests, and mainnet forking. Use when testing Solidity contracts, setting up blockchain test suites, or validating DeFi protocols.
solidity-security
Master smart contract security best practices to prevent common vulnerabilities and implement secure Solidity patterns. Use when writing smart contracts, auditing existing contracts, or implementing security measures for blockchain applications.
scikit-learn
ML toolkit. Classification, regression, clustering, PCA, preprocessing, pipelines, GridSearch, cross-validation, RandomForest, SVM, for general machine learning workflows.
scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
scanpy
Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
reportlab
PDF generation toolkit. Create invoices, reports, certificates, forms, charts, tables, barcodes, QR codes, Canvas/Platypus APIs, for professional document automation.
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