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Query and annotate gene variants from ClinVar and dbSNP databases. \n\.

This skill is applicable when using LaminDB. LaminDB is an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR-compliant. It is suitable for managing biological datasets (scRNA-seq, spatial transcriptomics, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakes, or ensuring data lineage and reproducibility in biological research. It covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integration with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

Utilities for querying the NCBI ClinVar database to retrieve variant records, clinical significance, and phenotype relationships; use when searching variants by gene/condition/significance, interpreting Pathogenic/Benign/VUS classifications, or annotating VCF files with ClinVar annotations.

Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.

Rank open GitHub issues by engagement and plan the selected issue.

Draft a single reply that addresses a processed issue-comment list, confirm with the user, and post it as a new PR issue comment.

R&R cycle — classify referee comments and route to appropriate agents. Replaces /respond-to-referee.

Creates a structured annotation note in references/ with sections for research question, data, findings, and relevance. Use when documenting a paper.

Drafts a point-by-point response letter to referee comments with suggested edits. Use after a revise-and-resubmit.

Access nucleotide sequence data from the European Nucleotide Archive

Query gene, sequence, and variant data via the Ensembl REST API

Browse and search Gene Ontology annotations via the QuickGO API

Legal document annotation, versioning, and analysis platform

Reference manager with PDF viewer and Markdown note support

Sync Zotero references and annotations to Notion databases

Guide to Zotero PDF Translate for multilingual PDF and annotation translation

Export Zotero items and annotations to Markdown note files

Python type hints and type safety patterns. Triggers on: type hints, typing, TypeVar, Generic, Protocol, mypy, pyright, type annotation, overload, TypedDict.

Auto-loaded context for Portfolio Buddy 2 development. Use for ANY task involving: React 19 development, TypeScript, portfolio analysis features, metrics calculations, trading strategy comparison, or working with the Portfolio Buddy 2 codebase. Contains tech stack, known issues, and architectural constraints.

Check if code is readable by non-developers - clear names, plain English comments, no jargon

Comprehensive PDF manipulation, extraction, and generation with support for text extraction, form filling, merging, splitting, annotations, and creation. Use when working with .pdf files for: (1) Extracting text and tables, (2) Filling PDF forms, (3) Merging/splitting PDFs, (4) Creating PDFs programmatically, (5) Adding watermarks/annotations, (6) PDF metadata management

Data validation and settings management using Python type annotations with Pydantic v2

This skill should be used when engineering decisions are being made during code implementation. The Archivist enforces decision documentation as a standard practice, ensuring every engineering choice includes rationale and integrates with Architecture Decision Records (ADRs). Use when writing code that involves choosing between alternatives, selecting technologies, designing architectures, or making trade-offs.

Write self-documenting code with minimal, evergreen comments that explain complex logic without describing recent changes or temporary fixes. Use this skill when writing code comments, documentation strings, explaining complex algorithms, clarifying business logic, or deciding whether code needs comments. Apply when working with any source code files where comments or documentation might be added, ensuring comments remain relevant, helpful, and focused on explaining why rather than what the code does, while preferring clear code structure and naming over excessive commenting.

Educational code development skill that teaches programming concepts while building applications. Use when the user wants to learn how code works, understand programming concepts, or build an app with detailed explanations. Provides line-by-line breakdowns, explains the 'why' behind code patterns, uses pedagogical teaching methods, and builds apps incrementally with educational commentary at each step.

Interacts with YouTrack issue tracker for IdeaVim. Use when working with tickets (VIM-XXXX), adding comments, managing tags, setting status, or release management. This project does NOT use GitHub Issues - use YouTrack instead.

Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.

Photo sharing platform for AI agents. Use this skill to share images, browse feeds, like posts, comment, and follow other agents. Requires ATXP authentication.

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Provides patterns for implementing Spring Boot caching: configures Redis/Caffeine/EhCache providers with TTL and eviction policies, applies @Cacheable/@CacheEvict/@CachePut annotations, validates cache hit/miss behavior, and exposes metrics via Actuator. Use when adding caching to Spring Boot services, configuring cache expiration, evicting stale data, or diagnosing cache misses.

Provides patterns to implement persistence layers with Spring Data JPA. Use when creating repositories, configuring entity relationships, writing queries (derived and `@Query`), setting up pagination, database auditing, transactions, UUID primary keys, multiple databases, and database indexing.

Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.

Parse, search, and modify HTML/XML documents by building a navigable tree of tags and text.

不安全代码与 FFI 专家。处理 unsafe, raw pointer, FFI, extern, transmute, *mut, *const, union, #[repr(C)], libc, MaybeUninit, NonNull, SAFETY comment, soundness, undefined behavior, UB, 安全抽象, 裸指针, 外部函数接口, 内存布局, 未定义行为

This skill should be used when users need to infer chromatin states from histone modification ChIP-seq data using chromHMM. It provides workflows for chromatin state segmentation, model training, state annotation.

This skill annotates chromatin loops, including enhancer/promoter assignments, CTCF-peak overlap. It automatically constructs enhancer and promoter sets when missing and outputs standardized loop categories.

Эксперт active learning. Используй для ML с участием человека, uncertainty sampling, annotation workflows и labeling optimization.

Add tweets with author linking, tags, and personal annotations.

Add Agentation visual feedback toolbar to a Next.js project

Collaborative programming framework for production-ready development. Use when starting features, writing code, handling security/errors, adding comments, discussing requirements, or encountering knowledge gaps. Applies to all development tasks for clear, safe, maintainable code.

Эксперт по data annotation. Используй для ML labeling, annotation workflows и quality control.

You are the Anchor Suggester skill. Your job is to help maintain high-quality documentation by proactively suggesting and adding anchor comments.

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

Imported skill app from langchain

Imported skill approval from langchain

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Automate backlink submission for directories, forums, and other non-blog resources using AI and browser automation

How to use bd (beads) for issue tracking, ready work, status updates, and comments in this repo.

Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.