Tools

Simple shell utilities for files and archives.

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 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.

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.

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.

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.

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.

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

Create new posts using the hydrate command.

Use when you need to work with database indexing.This skill provides index design and optimization with comprehensive guidance and automation.Trigger with phrases like "create indexes", "optimize indexes",or "improve query performance".

Compare staking rewards across validators and networks with ROI calculations.Use when optimizing proof-of-stake rewards.Trigger with phrases like "optimize staking", "compare validators", or "calculate rewards".

Use when you need to work with monitoring and observability.This skill provides health monitoring and alerting with comprehensive guidance and automation.Trigger with phrases like "monitor system health", "set up alerts",or "track metrics".