Skill Catalog
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Software Engineering
Ruby MCP Server Development Guidelines
Best practices and patterns for building Model Context Protocol (MCP) servers in Ruby using the official MCP Ruby SDK gem.
Ruby MCP Server Generator
Generate a complete Model Context Protocol server project in Ruby using the official MCP Ruby SDK gem.
Ruff Recursive Fix
Run Ruff checks with optional scope and rule overrides, apply safe and unsafe autofixes iteratively, review each change, and resolve remaining findings with targeted edits or user decisions.
Rust Async Patterns
Master Rust async programming with Tokio, async traits, error handling, and concurrent patterns. Use when building async Rust applications, implementing concurrent systems, or debugging async code.
Rust Coding Conventions and Best Practices
Rust programming language coding conventions and best practices
Rust Engineer
Writes, reviews, and debugs idiomatic Rust code with memory safety and zero-cost abstractions. Implements ownership patterns, manages lifetimes, designs trait hierarchies, builds async applications with tokio, and structures error handling with Result/Option. Use when building Rust applications, solving ownership or borrowing issues, designing trait-based APIs, implementing async/await concurrency, creating FFI bindings, or optimizing for performance and memory safety. Invoke for Rust, Cargo, ownership, borrowing, lifetimes, async Rust, tokio, zero-cost abstractions, memory safety, systems programming.
Rust MCP Expert
Expert assistant for Rust MCP server development using the rmcp SDK with tokio async runtime
Rust MCP Server Development Best Practices
Best practices for building Model Context Protocol servers in Rust using the official rmcp SDK with async/await patterns
Rust MCP Server Generator
Generate a complete Rust Model Context Protocol server project with tools, prompts, resources, and tests using the official rmcp SDK
SaaS Scaffolder
Generates complete, production-ready SaaS project boilerplate including authentication, database schemas, billing integration, API routes, and a working dashboard using Next.js 14+ App Router, TypeScript, Tailwind CSS, shadcn/ui, Drizzle ORM, and Stripe. Use when the user wants to create a new SaaS app, start a subscription-based web project, scaffold a Next.js application, or mentions terms like starter template, boilerplate, new project, or wiring up auth and payments.
Safe Database Schema Migration
Plan, execute, and verify database schema changes safely — without downtime, data loss, or rollback nightmares.
Saga Orchestration
Implement saga patterns for distributed transactions and cross-aggregate workflows. Use this skill when implementing distributed transactions across microservices where 2PC is unavailable, designing compensating actions for failed order workflows that span inventory, payment, and shipping services, building event-driven saga coordinators for travel booking systems that must roll back hotel, flight, and car rental reservations atomically, or debugging stuck saga states in production where compensation steps never complete.
Salesforce Apex Quality
Apex code quality guardrails for Salesforce development. Enforces bulk-safety rules (no SOQL/DML in loops), sharing model requirements, CRUD/FLS security, SOQL injection prevention, PNB test coverage (Positive / Negative / Bulk), and modern Apex idioms. Use this skill when reviewing or generating Apex classes, trigger handlers, batch jobs, or test classes to catch governor limit risks, security gaps, and quality issues before deployment.
Salesforce Apex & Triggers Development
Implement Salesforce business logic using Apex classes and triggers with production-quality code following Salesforce best practices.
Salesforce Component Standards
Quality standards for Salesforce Lightning Web Components (LWC), Aura components, and Visualforce pages. Covers SLDS 2 compliance, accessibility (WCAG 2.1 AA), data access pattern selection, component communication rules, XSS prevention, CSRF enforcement, FLS/CRUD in AuraEnabled methods, view state management, and Jest test requirements. Use this skill when building or reviewing any Salesforce UI component to enforce platform-specific security and quality standards.
Salesforce Developer
Writes and debugs Apex code, builds Lightning Web Components, optimizes SOQL queries, implements triggers, batch jobs, platform events, and integrations on the Salesforce platform. Use when developing Salesforce applications, customizing CRM workflows, managing governor limits, bulk processing, or setting up Salesforce DX and CI/CD pipelines.
Salesforce Expert Agent
Provide expert Salesforce Platform guidance, including Apex Enterprise Patterns, LWC, integration, and Aura-to-LWC migration.
Salesforce Flow Design
Salesforce Flow architecture decisions, flow type selection, bulk safety validation, and fault handling standards. Use this skill when designing or reviewing Record-Triggered, Screen, Autolaunched, Scheduled, or Platform Event flows to ensure correct type selection, no DML/Get Records in loops, proper fault connectors on all data-changing elements, and appropriate automation density checks before deployment.
Salesforce Flow Development
Implement business automation using Salesforce Flow following declarative automation best practices.
Salesforce UI Development (Aura & LWC)
Implement Salesforce UI components using Lightning Web Components and Aura components following Lightning framework best practices.
Salesforce Visualforce Development
Implement Visualforce pages and controllers following Salesforce MVC architecture and best practices.
Sandbox npm Install
Install npm packages in a Docker sandbox environment. Use this skill whenever you need to install, reinstall, or update node_modules inside a container where the workspace is mounted via virtiofs. Native binaries (esbuild, lightningcss, rollup) crash on virtiofs, so packages must be installed on the local ext4 filesystem and symlinked back.
Sanity Best Practices
Sanity development best practices for schema design, GROQ queries, TypeGen, Visual Editing, images, Portable Text, Studio structure, localization, migrations, Sanity Functions, Blueprints, and framework integrations such as Next.js, Nuxt, Astro, Remix, SvelteKit, Angular, Hydrogen, and the App SDK. Use this skill whenever working with Sanity schemas, defineType or defineField, GROQ or defineQuery, content modeling, Presentation or preview setups, Sanity-powered frontend integrations, Sanity Functions, documentEventHandler, defineDocumentFunction, defineMediaLibraryAssetFunction, @sanity/functions, @sanity/blueprints, sanity.blueprint.ts, event-driven content automation, or when reviewing and fixing a Sanity codebase.
Sanity Check
Step back, reflect on current work, validate direction and alignment. Use when complexity is increasing, feeling uncertain, before major decisions, or something feels off.
Scaffolding Oracle To Postgres Migration Test Project
Scaffolds an xUnit integration test project for validating Oracle-to-PostgreSQL database migration behavior in .NET solutions. Creates the test project, transaction-rollback base class, and seed data manager. Use when setting up test infrastructure before writing migration integration tests, or when a test project is needed for Oracle-to-PostgreSQL validation.
Scala Best Practices
Scala 2.12/2.13 programming language coding conventions and best practices following Databricks style guide for functional programming, type safety, and production code quality.
Schema
Designing database schemas, planning migrations, and authoring ER diagrams. Handles normalization, index strategies, and relation definitions. Use when DB schema design is needed.
Scout
Investigating bugs via root cause analysis (RCA), reproduction steps, and impact assessment. Investigation-only — identifies why bugs occur and where to fix them, no code. Use when a bug needs RCA, reproduction must be established before fix, or impact radius needs assessment.
Scribe
Authoring specifications, design documents, implementation checklists, and test specifications. Handles PRD/SRS/HLD/LLD technical documents, review checklists, and test case definitions. Does not write code. Use when technical documentation is needed.
Scrum Master
Advanced Scrum Master skill for data-driven agile team analysis and coaching. Use when the user asks about sprint planning, velocity tracking, retrospectives, standup facilitation, backlog grooming, story points, burndown charts, blocker resolution, or agile team health. Runs Python scripts to analyse sprint JSON exports from Jira or similar tools: velocity_analyzer.py for Monte Carlo sprint forecasting, sprint_health_scorer.py for multi-dimension health scoring, and retrospective_analyzer.py for action-item and theme tracking. Produces confidence-interval forecasts, health grade reports, and improvement-velocity trends for high-performing Scrum teams.
SE: Architect
System architecture review specialist with Well-Architected frameworks, design validation, and scalability analysis for AI and distributed systems
DevOps & Cloud
Run Acceptance Tests
Guide for running acceptance tests for a Terraform provider. Use this when asked to run an acceptance test or to run a test with the prefix `TestAcc`.
Runbook
Create or update an operational runbook for a recurring task or procedure. Use when documenting a task that on-call or ops needs to run repeatably, turning tribal knowledge into exact step-by-step commands, adding troubleshooting and rollback steps to an existing procedure, or writing escalation paths for when things go wrong.
Runbook
Create or load an operational runbook for a given topic. Searches `runbooks/` for an existing match; if none, scaffolds a new one from the standard template (Purpose / Prerequisites / Steps / Verification / Troubleshooting / Last Tested). Use when asked to "create a runbook", "load runbook for X", document a procedure, or look up an SOP.
Sandbox SDK
Build sandboxed applications for secure code execution. Load when building AI code execution, code interpreters, CI/CD systems, interactive dev environments, or executing untrusted code. Covers Sandbox SDK lifecycle, commands, files, code interpreter, and preview URLs. Biases towards retrieval from Cloudflare docs over pre-trained knowledge.
Scaffold
Provisioning infrastructure via cloud IaC (Terraform/OpenTofu/CloudFormation/Pulumi) and local development environments (Docker Compose/dev setup/env vars). Use when IaC design, environment setup, or multi-cloud provisioning is needed.
Scanning Containers With Trivy In Cicd
This skill covers integrating Aqua Security's Trivy scanner into CI/CD pipelines for comprehensive container image vulnerability detection. It addresses scanning Docker images for OS package and application dependency CVEs, detecting misconfigurations in Dockerfiles, scanning filesystem and git repositories, and establishing severity-based quality gates that block deployment of vulnerable images.
Data, AI & Research
Run Experiment
Deploy and run ML experiments on local or remote GPU servers. Use when user says "run experiment", "deploy to server", "跑实验", or needs to launch training jobs.
Run Experiment
Deploy and run ML experiments on local, remote, Vast.ai, or Modal serverless GPU. Use when user says "run experiment", "deploy to server", "跑实验", or needs to launch training jobs.
Run Models
Run AI models on Replicate via predictions, webhooks, and streaming.
Running Dbt Commands
Formats and executes dbt CLI commands, selects the correct dbt executable, and structures command parameters. Use when running models, tests, builds, compiles, or show queries via dbt CLI. Use when unsure which dbt executable to use or how to format command parameters.
Sag
ElevenLabs text-to-speech with mac-style say UX.
Scandinavia Transit
Search trains, buses, and ferries in Norway (Entur), Sweden (ResRobot), and Denmark (Rejseplanen). Intra-Scandinavia ground transport with schedules and Danish fare pricing.
Scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
Scientific Brainstorming
Open-ended scientific ideation partner. Use for research gaps, mechanism exploration, interdisciplinary connections, assumptions, possible research directions, and lightweight literature matrix or A+B paper-combination idea mapping. For structured testable hypotheses and validation plans, use hypothesis-generation instead.
Scientific Critical Thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
Scientific Critical Thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
Scientific Data Preprocessing
⚠️ CRITICAL USER EXPERIENCE-BASED SKILL - ALWAYS CONSULT BEFORE DATA PREPROCESSING ⚠️ Prevents catastrophic errors (88.9% error rate in V1.0 case study) through multi-level feature analysis, data leakage detection, and semantic validation. MANDATORY for: data preprocessing, feature engineering, standardization, normalization, interpolation, missing value handling, feature selection, or ANY data transformation task. Covers grouped time-series, cross-sectional, panel data. Detects: time travel leakage, causal inversion, ID misuse, semantic-numeric fallacies, distribution blindness. User's hard-won lessons from real project failures.
Scientific Paper Research
Research agent that searches scientific papers and retrieves structured experimental data from full-text studies using the BGPT MCP server.
Scientific Visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
Scientific Visualization
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
Scikit Learn
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.
Scikit Survival
Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.
Scipy Optimization
Optimize pump designs and system parameters using scipy.optimize
Scvelo
RNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and identify driver genes in single-cell RNA-seq data. Complements Scanpy/scVI-tools for trajectory inference.
Scvi Tools
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
Seaborn
Statistical visualization. Scatter, box, violin, heatmaps, pair plots, regression, correlation matrices, KDE, faceted plots, for exploratory analysis and publication figures.
Seaborn
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.
Searxng Search
Free meta-search via SearXNG — aggregates results from 70+ search engines. Self-hosted or use a public instance. No API key needed. Falls back automatically when the web search toolset is unavailable.
Seatmaps
Aircraft seat maps, cabin dimensions, and seat recommendations via SeatMaps.com and AeroLOPA. Search by flight number or airline+aircraft via agent-browser.
Seats Aero
Search award flight availability across 27 mileage programs via Seats.aero Partner API. Find cheapest award flights, compare programs, and get booking links.
Education & Writing
Ru Text
Use when writing, editing, or reviewing Russian-language text, or when user mentions ru-text. Covers typography, info-style, editorial, UX writing, business correspondence. Auto-activates on Russian text output.
Scaffold Exercises
Create exercise directory structures with sections, problems, solutions, and explainers that pass linting. Use when user wants to scaffold exercises, create exercise stubs, or set up a new course section.
Scholar Evaluation
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.
Scholarly Publishing
Use when planning an end-to-end scholarly publishing workflow, including manuscript source-of-truth, submission assets, revision/rebuttal files, camera-ready checks, reproducible build expectations, and publication package structure.
Scientific Reporting
Write research/technical reports with strong structure + figure standards. Supports Markdown/HTML/PDF outputs (Quarto optional), executive summary, methods, results, discussion, and reproducibility appendix.
Scientific Writing
Use when writing or revising scientific manuscript prose: IMRAD sections, abstracts, figure/table captions, citation-integrated paragraphs, reporting-guideline language, terminology, clarity, and journal-submission text.
Business, Marketing & Sales
SaaS Metrics
SaaS business metrics analysis - MRR, ARR, Churn, LTV, CAC, cohort analysis, and investor reporting
SaaS Metrics Coach
SaaS financial health advisor. Use when a user shares revenue or customer numbers, or mentions ARR, MRR, churn, LTV, CAC, NRR, or asks how their SaaS business is doing.
SaaS Valuation Compression
Analyze SaaS company valuation compression between funding rounds. Use this skill whenever the user asks about: how much a SaaS company's valuation multiple changed between rounds, why the ARR multiple compressed or expanded, comparing a company's compression to macro benchmarks, or explaining what drove valuation changes for any VC-backed software company. Trigger on phrases like "valuation compression", "ARR multiple", "round-to-round valuation", "multiple change", or when the user asks to compare a company's funding rounds. Always use this skill for any multi-round SaaS valuation analysis — do not try to answer from memory alone.
Sage
Advising founders YC-style by surfacing the #1 bottleneck via socratic probing, giving pattern-matched honest feedback, detecting founder anti-patterns, and extracting 1-2 week action items. Use when seeking founder-mode advisory. Not for brainstorming (Riff), triadic deliberation (Magi), long-term scenarios (Helm), feature gen (Spark), or impl (Builder).
Sales Enablement
When the user wants to create sales collateral, pitch decks, one-pagers, objection handling docs, or demo scripts. Also use when the user mentions 'sales deck,' 'pitch deck,' 'one-pager,' 'leave-behind,' 'objection handling,' 'deal-specific ROI analysis,' 'demo script,' 'talk track,' 'sales playbook,' 'proposal template,' 'buyer persona card,' 'help my sales team,' 'sales materials,' or 'what should I give my sales reps.' Use this for any document or asset that helps a sales team close deals. For competitor comparison pages and battle cards, see competitors. For marketing website copy, see copywriting. For cold outreach emails, see cold-email. For the offer being sold (bonuses, guarantees, pricing structure), see offers.
Scenario Analyzer
Skill that analyzes 18-month scenarios from a news headline. Runs the primary analysis with the scenario-analyst agent and obtains a second opinion with the strategy-reviewer agent. Generates a comprehensive English report covering 1st/2nd/3rd-order impacts, recommended stocks, and a critical review. Example: /scenario-analyzer "Fed raises rates by 50bp" Triggers: news analysis, scenario analysis, 18-month outlook, medium-to-long-term investment strategy
Scenario War Room
Cross-functional what-if modeling for cascading multi-variable scenarios. Unlike single-assumption stress testing, this models compound adversity across all business functions simultaneously. Use when facing complex risk scenarios, strategic decisions with major downside, or when the user asks 'what if X AND Y both happen?'
Schema
When the user wants to add, fix, or optimize schema markup and structured data on their site. Also use when the user mentions "schema markup," "structured data," "JSON-LD," "rich snippets," "schema.org," "FAQ schema," "product schema," "review schema," "breadcrumb schema," "Google rich results," "knowledge panel," "star ratings in search," or "add structured data." Use this whenever someone wants their pages to show enhanced results in Google. For broader SEO issues, see seo-audit. For AI search optimization, see ai-seo.
Schema Markup
When the user wants to implement, audit, or validate structured data (schema markup) on their website. Use when the user mentions 'structured data,' 'schema.org,' 'JSON-LD,' 'rich results,' 'rich snippets,' 'schema markup,' 'FAQ schema,' 'Product schema,' 'HowTo schema,' or 'structured data errors in Search Console.' Also use when someone asks why their content isn't showing rich results or wants to improve AI search visibility. NOT for general SEO audits (use seo-audit) or technical SEO crawl issues (use site-architecture).
Screenshot Optimization
When the user wants to design, optimize, or evaluate App Store screenshots and preview videos. Also use when the user mentions "screenshots", "app preview", "product page design", "screenshot design", "creative assets", or "what should my screenshots show". For A/B testing screenshots, see ab-test-store-listing. For full ASO audit, see aso-audit.
Seasonal Aso
When the user wants to optimize their App Store listing for seasonal events, holidays, or trending moments — including keyword opportunities, metadata updates, screenshot theming, and timing strategy. Use when the user mentions "seasonal", "holiday", "Christmas", "New Year", "Valentine's Day", "summer", "back to school", "seasonal keywords", "trending now", "limited time", or wants to capitalize on a calendar event. For general keyword research, see keyword-research. For full metadata rewrites, see metadata-optimization.
Web & Browser Automation
Safe Browser
Build local constrained-browser agents with a safe_browser tool that owns CDP, enforces a domain allowlist with Fetch interception, and lets a runtime Claude Agent SDK agent complete browsing tasks without raw browser, shell, or CDP access. Use when the user wants an agent to browse or scrape while staying on approved domains, demo blocked off-domain navigation, or generate a safe browser client.
Scanner Bridge
Internal helper agent. Invoked by orchestrator agents via Task tool. Internal helper that bridges GitHub Accessibility Scanner CI data with the agent ecosystem. Fetches scanner-created issues, normalizes findings, deduplicates against local scans, and tracks Copilot fix status.
Scrapling
CLI-first web scraping & content extraction with optional MCP server. Use when you have target URLs and need clean, selector-based outputs (html/md/txt).
Scrapling
Web scraping with Scrapling - HTTP fetching, stealth browser automation, Cloudflare bypass, and spider crawling via CLI and Python.
Scrapling Skill
Install, troubleshoot, and use Scrapling CLI to extract HTML, Markdown, or text from webpages. Use this skill whenever the user mentions Scrapling, `uv tool install scrapling`, `scrapling extract`, WeChat/mp.weixin articles, browser-backed page fetching, or needs help deciding between static and dynamic extraction.
Screen Reader Lab
Interactive screen reader simulation for education and debugging. Parses HTML/JSX and produces step-by-step narration of what a screen reader would announce. Supports reading order, Tab navigation, heading navigation (H key), and form navigation (F key) modes. Not a replacement for real screen reader testing.
Screen Reader Testing
Test web applications with screen readers including VoiceOver, NVDA, and JAWS. Use when validating screen reader compatibility, debugging accessibility issues, or ensuring assistive technology support.
Security & Compliance
Safe Encryption
Encrypt, decrypt, and manage keys with the SAFE CLI — a modern GPG alternative with post-quantum support.
Sast Sca Security Analyzer
Use when: performing SAST (Static Application Security Testing), SCA (Software Composition Analysis), scanning source code or binaries for security flaws, auditing third-party dependency vulnerabilities, checking policy compliance, generating structured security reports, identifying CWE-mapped flaws with file/line precision, reviewing open-source license risk, or producing CI/CD-gate security findings.
Scanning Container Images With Grype
Scan container images for known vulnerabilities using Anchore Grype with SBOM-based matching and configurable severity thresholds.
Scanning Docker Images With Trivy
Trivy is a comprehensive open-source vulnerability scanner by Aqua Security that detects vulnerabilities in OS packages, language-specific dependencies, misconfigurations, secrets, and license violati
Scanning Infrastructure With Nessus
Tenable Nessus is the industry-leading vulnerability scanner used to identify security weaknesses across network infrastructure including servers, workstations, network devices, and operating systems.
Scanning Kubernetes Manifests With Kubesec
Perform security risk analysis on Kubernetes resource manifests using Kubesec to identify misconfigurations, privilege escalation risks, and deviations from security best practices.
Scanning Network With Nmap Advanced
Performs advanced network reconnaissance using Nmap's scripting engine, timing controls, evasion techniques, and output parsing to discover hosts, enumerate services, detect vulnerabilities, and fingerprint operating systems across authorized target networks.
Personal Productivity
Salary Negotiation Prep
Research market rates, build negotiation strategy, and create counter-offer scripts
Savings Goals
Plan and track savings for specific financial goals including retirement, education, and home purchase. Use when the user asks about required savings rates, 529 plans, retirement accumulation targets, down payment planning, or goal prioritization. Also trigger when users mention 'how much do I need to save each month', 'am I on track for retirement', 'college savings', 'safe withdrawal rate', '4% rule', 'FIRE savings rate', 'catch-up contributions', 'employer match', or ask how to balance competing savings goals.
Scale Recipe
Adjust recipe servings and display scaled ingredient quantities
Screenshot
Use when the user explicitly asks for a desktop or system screenshot (full screen, specific app or window, or a pixel region), or when tool-specific capture capabilities are unavailable and an OS-level capture is needed.
Science & Simulation
Scanpy
Single-cell RNA-seq and retained scverse workflow owner. Load .h5ad/10X data, manage AnnData metadata, plan scVI/scANVI batch-correction workflows, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.
Scientific Brainstorming
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.
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.