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Found 352 Skills
Retrieves gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation, experiment quality assessment, and structured reports. Creates comprehensive dataset profiles with metadata, sample information, and download links. Use when users need expression data, omics datasets, or mention ArrayExpress (E-MTAB, E-GEOD) or BioStudies (S-BSST) accessions.
Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.
Comprehensive DeepResearch methodology for conducting rigorous, traceable research projects with quality gates, structured analysis, and decision-ready deliverables. Use when (1) Conducting deep research projects requiring evidence-based analysis, (2) Managing research progress with quality gates and artifacts, (3) Producing research reports with traceable sources and structured reasoning, (4) Applying OSINT verification techniques, (5) Using structured analytic techniques (ACH, Key Assumptions Check, Red Team), (6) Expressing uncertainty and confidence in research findings, (7) Ensuring research deliverables meet intelligence tradecraft standards (ICD 203/206/208)
Converts long inline XAML bindings to Property Element Syntax for better readability. Use when XAML binding expressions become too long or complex.
Perl text processing and scripting with regular expressions. Use for .pl files.
Build applications using the x402 protocol — Coinbase's open standard for HTTP-native stablecoin payments using the HTTP 402 status code. Use this skill when: - Creating APIs that require USDC payments per request (seller/server side) - Building clients or AI agents that pay for x402-protected resources (buyer/client side) - Implementing MCP servers with paid tools for Claude Desktop - Adding payment middleware to Express, Hono, or Next.js applications - Working with Base (EVM) or Solana (SVM) payment flows - Building machine-to-machine or agent-to-agent payment systems - Integrating micropayments, pay-per-use billing, or paid API access Triggers: x402, HTTP 402, payment required, USDC payments, micropayments, pay-per-use API, agentic payments, stablecoin payments, paid API endpoint, paywall middleware
Generate production-ready monorepo structures for full-stack applications including frontends (Next.js, React), APIs (Hono, Express), and data pipelines. Use when creating new monorepo projects, scaffolding multi-project architectures (web apps, APIs, workers, CLI tools), setting up shared packages, or configuring workspace tooling with Bun, PNPM, or Yarn.
Better Auth — framework-agnostic TypeScript authentication & authorization library. Covers setup, email/password, social OAuth (40+ providers), passkeys, magic links, 2FA, organizations, sessions, plugins, admin, hooks, and security hardening. Use when implementing auth with Better Auth: configuring auth instances, adding providers, setting up database adapters (Prisma, Drizzle, PostgreSQL, MySQL, SQLite, MongoDB), integrating with frameworks (Next.js, Nuxt, SvelteKit, Astro, Hono, Express, Elysia, Fastify, Expo), managing sessions, or extending with plugins.
Integrate and analyze multiple omics datasets (transcriptomics, proteomics, epigenomics, genomics, metabolomics) for systems biology and precision medicine. Performs cross-omics correlation, multi-omics clustering (MOFA+, NMF), pathway-level integration, and sample matching. Coordinates ToolUniverse skills for expression data (RNA-seq), epigenomics (methylation, ChIP-seq), variants (SNVs, CNVs), protein interactions, and pathway enrichment. Use when analyzing multi-omics datasets, performing integrative analysis, discovering multi-omics biomarkers, studying disease mechanisms across molecular layers, or conducting systems biology research that requires coordinated analysis of transcriptome, genome, epigenome, proteome, and metabolome data.
Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering. Handles multi-factor designs, multiple contrasts, batch effects, and integrates with gene enrichment (gseapy) and ToolUniverse annotation tools (UniProt, Ensembl, OpenTargets). Supports CSV/TSV/H5AD input formats and any organism. Use when analyzing RNA-seq count matrices, identifying DEGs, performing differential expression with statistical rigor, or answering questions about gene expression changes.
Analyze mass spectrometry proteomics data including protein quantification, differential expression, post-translational modifications (PTMs), and protein-protein interactions. Processes MaxQuant, Spectronaut, DIA-NN, and other MS platform outputs. Performs normalization, statistical analysis, pathway enrichment, and integration with transcriptomics. Use when analyzing proteomics data, comparing protein abundance between conditions, identifying PTM changes, studying protein complexes, integrating protein and RNA data, discovering protein biomarkers, or conducting quantitative proteomics experiments.
Design and build SuperPlane workflow canvases from requirements. Translates workflow descriptions into canvas YAML with triggers, components, edges, and expressions. Use when the user wants to create a new workflow, build a canvas, design a pipeline, or wire up components. Triggers on "build canvas", "create workflow", "design pipeline", "automate".