Comments
Code comments and annotations
packages-documentation
by reactive
Write, update, and format docs for public APIs - API reference, README, docstrings, usage examples, migration guides, deprecation notices
issues-deduplication
by JetBrains
Handles deduplication of YouTrack issues. Use when cleaning up duplicate issues, consolidating related bug reports, or organizing issue tracker.
tests-maintenance
by JetBrains
Maintains IdeaVim test suite quality. Reviews disabled tests, ensures Neovim annotations are documented, and improves test readability. Use for periodic test maintenance.
extensions-api-migration
by JetBrains
Migrates IdeaVim extensions from the old VimExtensionFacade API to the new @VimPlugin annotation-based API. Use when converting existing extensions to use the new API patterns.
tcga-bulk-data-preprocessing-with-omicverse
by Starlitnightly
Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.
spring-boot-openapi-documentation
by giuseppe-trisciuoglio
Provides patterns to generate comprehensive REST API documentation using SpringDoc OpenAPI 3.0 and Swagger UI in Spring Boot 3.x applications. Use when setting up API documentation, configuring Swagger UI, adding OpenAPI annotations, implementing security documentation, or enhancing REST endpoints with examples and schemas.
langchain4j-ai-services-patterns
by giuseppe-trisciuoglio
Provides patterns to build declarative AI Services with LangChain4j using interface-based patterns, annotations, memory management, tools integration, and advanced application patterns. Use when implementing type-safe AI-powered features with minimal boilerplate code in Java applications.
ai-summary-comment
by dotnet
Posts or updates automated progress comments on GitHub PRs. Use after completing any PR agent phase (pre-flight, tests, gate, fix, report). Triggers on 'post comment to PR', 'update PR progress', 'comment on PR with results', 'post pre-flight comment'. Creates single aggregated review comment with collapsible sections per commit.
geo-database
by jaechang-hits
"Query NCBI Gene Expression Omnibus (GEO) for gene expression datasets and sample metadata via GEOparse Python library and E-utilities. Search datasets by keyword/organism/platform, download GSE series matrices, parse GPL platform annotations, extract GSM sample metadata, and load expression matrices into pandas. For single-cell data use cellxgene-census; for programmatic multi-DB access use gget-genomic-databases."
omero-integration
by jaechang-hits
"OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with tags and key-value pairs, manage ROIs, and integrate OMERO image data into downstream analysis pipelines — all programmatically without the OMERO desktop GUI."
etetoolkit
by jaechang-hits
"ETE Toolkit (ETE3) is a Python environment for phylogenetic tree analysis, manipulation, and visualization. Parse Newick/NHX/PhyloXML trees, traverse and annotate nodes, render publication-quality figures with TreeStyle/NodeStyle, integrate NCBI taxonomy for taxon-aware operations, and run PhyloTree workflows for comparative genomics. Use for building species trees, gene family evolution analysis, and annotated tree figures."
cosmic-database
by jaechang-hits
"Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity."
napari-image-viewer
by jaechang-hits
"Interactive multi-dimensional image viewer for scientific microscopy data. Napari displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, and Tracks layers; supports real-time annotation, plugin-based analysis, and headless screenshot export. Core visualization tool for bioimage analysis workflows. Use ImageJ/FIJI for macro-based processing; use napari for Python-native interactive visualization and plugin-based deep learning segmentation review."
celltypist-cell-annotation
by jaechang-hits
"Automated cell type annotation for scRNA-seq data using pre-trained logistic regression models. CellTypist ships 45+ models covering immune cells, gut, lung, brain, fetal tissues, and cancer microenvironments. Inputs a normalized AnnData; outputs per-cell predicted labels, majority-vote cluster labels, and confidence scores. Use when you want fast, reproducible, reference-model-backed annotation without manual marker inspection."
ontology-validator
by HeshamFS
Validate material sample annotations and data structures against ontology constraints. Use when checking if CMSO annotations are correct, verifying that required properties are present, or validating that object property relationships have consistent domain and range. Catches unknown classes, unknown properties, domain mismatches, and missing required fields.
single-cell-cellphonedb-communication-mapping
by Starlitnightly
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
annotations
by dropseed
Workflow for adding type annotations to Plain packages. Use this when adding or improving type coverage.
testing-hashql
by hashintel
HashQL testing strategies including compiletest (UI tests), unit tests, and snapshot tests. Use when writing tests for HashQL code, using //~ annotations, running --bless, debugging test failures, or choosing the right testing approach.
linkedin-content
by inference-sh
"LinkedIn post writing with hook formulas, formatting rules, and engagement patterns. Covers post types, algorithm signals, character limits, and content pillars. Use for: LinkedIn posts, professional content, thought leadership, B2B content, personal branding. Triggers: linkedin post, linkedin content, linkedin writing, linkedin strategy, linkedin engagement, linkedin algorithm, linkedin hook, linkedin formatting, thought leadership, professional content, b2b content, linkedin growth"
data-visualization
by inference-sh
"Data visualization with chart selection, color theory, and annotation best practices. Covers chart types (bar, line, scatter, heatmap), axes rules, and storytelling with data. Use for: charts, graphs, dashboards, reports, presentations, infographics, data stories. Triggers: data visualization, chart, graph, data chart, bar chart, line chart, scatter plot, data viz, visualization, dashboard chart, infographic data, data presentation, chart design, plot, heatmap, pie chart alternative"
agentation
by benjitaylor
Add Agentation visual feedback toolbar to a Next.js project
pr-apply-review
by ryoppippi
Fetch and apply review comments from the current PR. Use when you need to address PR feedback.
.NET Conventions
by exceptionless
C# coding standards for the Exceptionless codebase. Naming conventions, async patterns, structured logging, nullable reference types, and formatting rules. Keywords: C# style, naming conventions, _camelCase, PascalCase, async suffix, CancellationToken, nullable annotations, structured logging, ExceptionlessState
code-walk-thru
by pchalasani
Use this when user wants you to walk through (code or text) files in a EDITOR to either explain how some code works, or to show the user what changes you made, etc. You would typically use this repeatedly to show the user your changes or code files one by one, sometimes with specific line-numbers. This way the user is easily able to follow along in their favorite EDITOR as you point at various files possibly at specific line numbers within those files.