medchem
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
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.
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.
scvi-tools
This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.
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.
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
pydeseq2
Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.
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.
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.
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.
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.
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.
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.
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.
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.
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.
meeting-insights-analyzer
Analyzes meeting transcripts and recordings to uncover behavioral patterns, communication insights, and actionable feedback. Identifies when you avoid conflict, use filler words, dominate conversations, or miss opportunities to listen. Perfect for professionals seeking to improve their communication and leadership skills.
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
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
Remembering Conversations
Search previous Claude Code conversations for facts, patterns, decisions, and context using semantic or text search
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
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
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.
bioservices
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).
biopython
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.
arboreto
Gene regulatory network inference with GRNBoost2/GENIE3 algorithms. Infer TF-target relationships from expression data, scalable with Dask, for scRNA-seq and GRN analysis.
algorithmic-art
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
webapp-testing
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
canvas-design
Create beautiful visual art in .png and .pdf documents using design philosophy. You should use this skill when the user asks to create a poster, piece of art, design, or other static piece. Create original visual designs, never copying existing artists' work to avoid copyright violations.
tooluniverse
Use this skill when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery. This skill provides access to 600+ scientific tools including machine learning models, datasets, APIs, and analysis packages. Use when searching for scientific tools, executing computational biology workflows, composing multi-step research pipelines, accessing databases like OpenTargets/PubChem/UniProt/PDB/ChEMBL, performing tool discovery for research tasks, or integrating scientific computational resources into LLM workflows.
Algorithmic Art Generation
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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.
uv-tdd
A development process for Python applications that uses TDD to iterate on a new project based around uv. Use when Claude needs to create a new Python project, write Python code with tests, or work on Python development using test-driven development practices with the uv package manager.
setup-to-pyproject
Migrate Python projects from setup.py/setup.cfg to pyproject.toml for use with uv. Use when upgrading legacy Python packaging, converting setup.py to modern pyproject.toml format, setting up dependency groups for development/testing, and ensuring `uv run pytest` works correctly.
cogapp-markdown
Use cogapp to auto-generate sections of markdown documentation by embedding Python code that produces content. Use when a project needs to keep documentation in sync with code, such as embedding CLI --help output in README files, generating tables, or any content that should be derived from the code itself rather than manually maintained.
upgrade-actions
Upgrade GitHub Actions workflows
verifying-with-storybook
Use when building or modifying SwiftUI views and need to visually verify the implementation matches requirements. Especially useful when implementing design specs, fixing UI bugs, or creating new components where visual correctness is critical.
cosmosdb-best-practices
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organize-project
Organize files and folders into QCut's standard project structure. Use when setting up a new project, cleaning up files, or when the user asks to organize their workspace.
pr-comments
Export, preprocess, and fix GitHub PR review comments. Use when user wants to export PR comments, evaluate code reviews, or fix review feedback from CodeRabbit/Gemini bots.
project-docs
AI Content Pipeline documentation and architecture reference. Use when understanding codebase structure, AI models, CLI commands, YAML pipelines, provider APIs, error codes, or finding implementation details.
migration-specialist
Migration specialist for zero-downtime schema changes, data migrations, and backward-compatible evolutionUse when "migration, schema change, database migration, zero downtime, backward compatible, rollback, blue green, data migration, migration, schema, database, zero-downtime, backward-compatible, rollback, blue-green, feature-flag, ml-memory" mentioned.
meme-engineering
Expert in meme creation and virality - understanding why certain ideas spread while others die. Covers meme formats, timing, adaptation, meta-commentary, and platform-specific optimization. Knows the difference between forcing a meme and engineering conditions for organic spread. Use when "meme, viral content, make it memeable, shareable, internet culture, template, " mentioned.
micro-saas-launcher
Expert in launching small, focused SaaS products fast - the indie hacker approach to building profitable software. Covers idea validation, MVP development, pricing, launch strategies, and growing to sustainable revenue. Ship in weeks, not months. Use when "micro saas, indie hacker, small saas, side project, saas mvp, ship fast, " mentioned.
microservices-patterns
Patterns for designing, building, and operating microservices architectures. Covers service decomposition, inter-service communication, resilience patterns, data consistency, and observability in distributed systems. Use when ", " mentioned.
neon-postgres
Expert patterns for Neon serverless Postgres, branching, connection pooling, and Prisma/Drizzle integrationUse when "neon database, serverless postgres, database branching, neon postgres, postgres serverless, connection pooling, preview environments, database per preview, neon, postgres, serverless, database, branching, prisma, drizzle, connection-pooling" mentioned.
negotiation-playbook
Expert in negotiation strategy - systematic approaches to reaching agreements that create value. Covers preparation, tactics, objection handling, and closing. Knows when to push, when to concede, and how to expand the pie rather than just divide it. Use when "negotiation, negotiate, deal terms, BATNA, making a deal, closing a deal, contract terms, bargaining, " mentioned.
narrative-design
The craft of weaving story into interactive systems where the player is both audience and author. This skill covers the unique challenges of game narrative: branching structures that respect player agency, environmental storytelling that rewards exploration, dialogue systems that feel alive, and the delicate balance between authored experience and emergent narrative. Unlike linear media, games don't tell stories TO players - they create the conditions for stories to emerge WITH players. The narrative designer's job is to build the scaffolding that supports infinite player-authored moments while maintaining coherent themes and emotional arcs. This skill synthesizes lessons from Disco Elysium's internal monologue as gameplay, Hades' death-as-narrative-engine, interactive fiction's branching mastery (Inkle, Twine), and procedural narrative pioneers like Dwarf Fortress. It addresses ludonarrative harmony, bark systems, cinematics that respect agency, and the "and therefore" test that separates plot from story. Use when "narrative design, game story, game writing, dialogue system, branching narrative, player choice, environmental storytelling, bark system, quest design, lore delivery, ludonarrative, interactive fiction, inkle, twine, dialogue tree, player agency, cinematic design, voice direction, localization, procedural narrative, narrative, game-writing, dialogue, branching, player-agency, environmental-storytelling, quest-design, voice-acting, localization, interactive-fiction, procedural-narrative, ludonarrative" mentioned.
multimodal-ai
Patterns for building multimodal AI applications that combine text, images, audio, and video. Covers vision APIs, audio transcription, and unified pipelines. Use when "multimodal AI, vision API, image understanding, GPT-4V, Claude vision, audio transcription, Whisper, document extraction, image to text, " mentioned.
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