Comprehensive PDF manipulation toolkit for extracting text and tables, creating new PDFs, merging/splitting documents, and handling forms. When Claude needs to fill in a PDF form or programmatically process, generate, or analyze PDF documents at scale.
pptx
Presentation creation, editing, and analysis. When Claude needs to work with presentations (.pptx files) for: (1) Creating new presentations, (2) Modifying or editing content, (3) Working with layouts, (4) Adding comments or speaker notes, or any other presentation tasks
xlsx
Comprehensive spreadsheet creation, editing, and analysis with support for formulas, formatting, data analysis, and visualization. When Claude needs to work with spreadsheets (.xlsx, .xlsm, .csv, .tsv, etc) for: (1) Creating new spreadsheets with formulas and formatting, (2) Reading or analyzing data, (3) Modify existing spreadsheets while preserving formulas, (4) Data analysis and visualization in spreadsheets, or (5) Recalculating formulas
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-writing
Write scientific manuscripts. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), abstracts, for research papers and journal submissions.
statistical-analysis
Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research.
ffuf-web-fuzzing
Expert guidance for ffuf web fuzzing during penetration testing, including authenticated fuzzing with raw requests, auto-calibration, and result analysis
hypothesis-generation
Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.
exploratory-data-analysis
EDA toolkit. Analyze CSV/Excel/JSON/Parquet files, statistical summaries, distributions, correlations, outliers, missing data, visualizations, markdown reports, for data profiling and insights.
protocolsio-integration
Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.
opentrons-integration
Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
latchbio-integration
Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
labarchive-integration
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
context-initialization
Always Auto-invoked skill that creates/updates workspace AGENTS.md to instruct the agent to always search for existing skills before attempting any scientific task.
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.
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
verification-before-completion
Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims; evidence before assertions always
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
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
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.).
scientific-brainstorming
Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving.
scientific-critical-thinking
Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims.
peer-review
Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.
figma-to-code
Generate production-ready React/Next.js code from Figma designs. Instructs proper Figma MCP tool usage, component reuse strategies, and variant mapping. **CRITICAL: ALWAYS use this skill when user provides a Figma link or mentions implementing/redesigning from Figma design.** Never attempt manual implementation without invoking this skill first.
gemini
This skill should be used when the user wants to invoke Google Gemini CLI for complex reasoning tasks, research, and AI assistance. Trigger phrases include "use gemini", "ask gemini", "run gemini", "call gemini", "gemini cli", "Google AI", "Gemini reasoning", or when users request Google's AI models, need advanced reasoning capabilities, research with web search, or want to continue previous Gemini conversations. Automatically triggers on Gemini-related requests and supports session continuation for iterative development.
codex
This skill should be used when the user wants to invoke Codex CLI for complex coding tasks requiring high reasoning capabilities. Trigger phrases include "use codex", "ask codex", "run codex", "call codex", "codex cli", "GPT-5 reasoning", "OpenAI reasoning", or when users request complex implementation challenges, advanced reasoning, architecture design, or high-reasoning model assistance. Automatically triggers on codex-related requests and supports session continuation for iterative development.
plan-executor
Execute implementation plans step-by-step. Use when user says "execute the plan", "implement the plan we created", "start building based on the plan", "go ahead and implement it", "proceed with the implementation", or references a plan file and wants to begin coding.
prompt-optimizer
Optimize prompts for better AI performance. Use when user says "improve this prompt for better results", "optimize this prompt to reduce tokens", "apply prompt engineering best practices to this", "make this prompt more effective", "help me refine this system prompt", or "tune this prompt for the AI model I'm using".
claude-docs-updater
Update CLAUDE.md documentation files after code changes. Use when user says "update the CLAUDE.md", "sync the docs with my changes", "document what I changed", "update documentation for this package", or after making significant code modifications that should be reflected in project documentation.
plan-swarm
Refine plans through multi-agent expert discussion. Use when user says "get multiple expert opinions on this plan", "I want different perspectives on this approach", "have the agents discuss this strategy", "refine the plan through collaborative review", or "what would different specialists think about this design".
plan-reviewer
Review implementation plans for completeness and feasibility. Use when user says "review this plan before I start", "is this implementation plan complete", "check if this plan aligns with our patterns", "give me feedback on my implementation strategy", or "validate this plan before we execute it".
pr-creator
Create or update pull requests with conventional commits. Use when user says "create a PR for these changes", "submit this for review", "open a pull request", "push these changes and create a PR", "I'm ready to submit this work", or "create PR and link to issue #123".
topic-researcher
Research external documentation and best practices. Use when user says "look up the docs for this library", "research best practices for implementing caching", "how do other projects handle authentication", "check the official documentation for this API", "compare our implementation with industry standards", or "what's the recommended way to structure this".
codebase-explorer
Explore and understand how the codebase works. Use when user asks "how does the authentication work", "where is the API endpoint defined", "show me how data flows through the system", "explain this module's architecture", "trace the request from controller to database", or "I need to understand this feature before making changes".
code-refactorer
Refactor code with safety checks and pattern application. Use when user says "refactor this code", "clean up this function", "simplify this logic", "extract this into a separate function", "apply the strategy pattern here", "reduce the complexity of this module", or "reorganize this file structure".
pr-issue-resolver
Fix PR issues including review comments and CI failures. Use when user says "fix the failing CI on my PR", "address the review comments on PR #123", "my PR has failing checks", "help me resolve the feedback on my pull request", "the build is failing on my PR", or "make my PR merge-ready".
pr-reviewer
Review pull requests for quality, security, and performance. Use when user says "review my changes before I merge", "do a code review on this PR", "check if this is ready to merge", "review the diff for any issues", "give me feedback on these changes", or "is this PR ready for review".
tech-debt-analyzer
Analyze and prioritize technical debt with remediation plans. Use when user says "analyze the technical debt in this codebase", "what's the code quality like in this module", "identify what's slowing down our development", "assess the maintenance burden of this legacy code", "create a plan to pay down our tech debt", or "where should we focus our cleanup efforts".
implementation-planner
Create implementation plans for features and changes. Use when user says "plan how to implement user authentication", "how should I add dark mode to the app", "what's the best way to refactor the database layer", "create a plan for migrating to the new API", or "I need to implement [feature] - help me plan it out".
graphite-stack-updater
Update Graphite PR stacks by addressing review comments and syncing PRs. Use when user says "update my graphite stack", "address the review comments on my stack", "sync my PR stack after these changes", "submit my entire stack to Graphite", or "I need to update all the PRs in my stack".
AgentStack
This is main documentation for the AgentStack skill, which provides instructions and guidelines for how to use this skill effectively in various scenarios.
data-validator
Validate data against schemas, business rules, and data quality standards.
csv-processor
Parse, transform, and analyze CSV files with advanced data manipulation capabilities.
conflict-resolver
Smart git merge conflict resolution with context analysis, pattern detection, and automated resol...
compliance-checker
Check code against security compliance standards and best practices.
complexity-analyzer
Measure and report code complexity metrics with actionable recommendations.
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