Claude Code plugin with specialized agents for scientific writing, code review, and technical documentation
Agent
Use this agent to scan code for specific architectural antipatterns and violations of clean code principles. This agent focuses on pattern detection and identification rather than comprehensive review. Examples: Context: User wants to check if their codebase has common antipatterns before refactoring. user: 'Can you…
Agent
Use this agent when you need expert code review focused on clean code principles, maintainability, and software craftsmanship. Examples: Context: The user has just written a new function and wants it reviewed for clean code principles. user: 'I just wrote this function to calculate user permissions. Can you review…
Agent
Use this agent to perform gentle code smell detection, identifying maintainability hints and readability improvements in a supportive, mentoring tone. This agent focuses on semantic issues that static analyzers miss, suggesting areas where code could be more expressive or maintainable. Examples: Context: User wants a…
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Use this agent when preparing a scientific manuscript for journal submission to perform final quality checks on repositories, references, and bibliographic information. Examples: (1) Context: User has completed a research paper and needs to verify all external resources before submission. User: 'I've finished my paper…
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Use this agent when you need to create mathematical summaries of statistical/computational content in pull requests. Examples: Context: User has just completed a PR with new clustering algorithms and wants mathematical documentation. user: 'I've finished implementing a new distance metric for phylogenetic trees in my…
Agent
Use this agent when you need to perform meticulous proofreading of PDF documents at the proof stage from academic journals. This agent is specifically designed for final-stage proofreading where only grammatical errors and typos can be corrected, without any rephrasing or meaning changes. Examples: Context: User has…
Agent
Use this agent when you need to analyze, extract information from, or answer questions about scientific PDFs. This includes tasks like finding specific research findings, summarizing methodologies, extracting data from tables/figures, comparing results across papers, or providing expert interpretation of scientific…
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Use this agent when you need expert scientific editing for LaTeX documents following the Matsen group's writing guidelines. Examples: Context: User has written a draft of a scientific paper section and wants it reviewed for clarity and style. user: 'I've finished writing the methods section of my paper. Can you review…
Agent
Use this agent when you need expert guidance on creating, reviewing, or optimizing Snakemake workflows and pipelines according to best practices. Examples: Context: The user is creating a new bioinformatics pipeline and wants to ensure it follows Snakemake best practices. user: 'I'm building a Snakemake workflow for…
Agent
Use this agent when you need meticulous grammar checking for LaTeX/TeX files, particularly for academic papers, theses, or technical documents. Examples: Context: User has written a section of their research paper and wants to ensure grammatical accuracy before submission. user: 'I just finished writing the…
Agent
Use this agent when you need to review LaTeX documents for verb tense consistency and correctness according to scientific writing standards. Examples: Context: User has just finished writing a methods section in their research paper. user: 'I just wrote the methods section for my paper. Can you check the verb tense?'…
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Use this agent when you need to improve paragraph structure in LaTeX documents by ensuring each paragraph starts with a strong topic sentence. Examples: Context: User has written several paragraphs in a research paper and wants to improve readability. user: 'I've finished writing the methods section, can you help make…