Tools

Simple shell utilities for files and archives.

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.

Map scRNA-seq atlases onto spatial transcriptomics slides using omicverse's Single2Spatial workflow for deep-forest training, spot-level assessment, and marker visualisation.

Guide Claude through SCSA, MetaTiME, CellVote, CellMatch, GPTAnno, and weighted KNN transfer workflows for annotating single-cell modalities.

Creates user-specific one-click action templates that execute email operations when clicked in the chat interface. Use when user wants reusable actions for their specific workflows (send payment reminder to ACME Corp, forward bugs to engineering, archive old newsletters from specific sources).

Guide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.

Guide to reproducing OmicVerse trajectory workflows spanning PAGA, Palantir, VIA, velocity coupling, and fate scoring notebooks.

Creates event-driven email listeners that monitor for specific conditions (like urgent emails from boss, newsletters to archive, package tracking) and execute custom actions. Use when user wants to be notified about emails, automatically handle certain emails, or set up email automation workflows.

Guide Claude through omicverse's single-cell clustering workflow, covering preprocessing, QC, multimethod clustering, topic modeling, cNMF, and cross-batch integration as demonstrated in t_cluster.ipynb and t_single_batch.ipynb.

Turn bulk RNA-seq cohorts into synthetic single-cell datasets using omicverse's Bulk2Single workflow for cell fraction estimation, beta-VAE generation, and quality control comparisons against reference scRNA-seq.

Expert Java developer skill for AgentScope Java framework - a reactive, message-driven multi-agent system built on Project Reactor. Use when working with reactive programming, LLM integration, agent orchestration, multi-agent systems, or when the user mentions AgentScope, ReActAgent, Mono/Flux, Project Reactor, or Java agent development. Specializes in non-blocking code, tool integration, hooks, pipelines, and production-ready agent applications.

Use when working on or reviewing session execution, command handling, shell state, FIFO-based streaming, or stdout/stderr separation. Relevant for session.ts, command handlers, exec/execStream, or anything involving shell process management. (project)

Use when creating git commits to ensure commit messages follow project standards. Applies the 7 rules for great commit messages with focus on conciseness and imperative mood.

Morning routine, midday check-in, and evening shutdown workflows. Structure daily planning, task review, and end-of-day reflection. Use for daily productivity routines.

Generate comprehensive, accurate API documentation from source code. Use when creating or updating API documentation, generating OpenAPI specs, or when users mention API docs, endpoints, or documentation.

Create new posts using the hydrate command.

Read files without making changes. Use when you need read-only file access.

Use when you need to work with security and compliance.This skill provides security scanning and vulnerability detection with comprehensive guidance and automation.Trigger with phrases like "scan for vulnerabilities", "implement security controls",or "audit security".

Analyze network latency and optimize request patterns for faster communication. Use when diagnosing slow network performance or optimizing API calls. Trigger with phrases like "analyze network latency", "optimize API calls", or "reduce network delays".

Enforce complete Taskwarrior integration for all coding tasks with automatic decomposition, time tracking, and dependency management. Use when managing tasks or tracking work. Trigger with phrases like "taskwarrior", "task warrior", "tw", "create a task", or "track this work".