BAM-filtration
Performs data cleaning and removal operations. This skill takes a raw BAM and creates a new, "clean" BAM file by actively removing artifacts: mitochondrial reads, blacklisted regions, PCR duplicates, and unmapped reads. Use this skill to "clean," "filter," or "remove bad reads" from a dataset. This is a prerequisite step before peak calling. Do NOT use this skill if you only want to view statistics without modifying the file.
replicates-incorporation
This skill manages experimental reproducibility, pooling, and consensus strategies. This skill operates in two distinct modes based on the input state. (1) Pre-Peak Calling (BAM Mode): It merges all BAMs, generate the merge BAM file to prepare for track generation and (if provided with >3 biological replicates) splits them into 2 balanced "pseudo-replicates" to prepare for peak calling. (2) Post-Peak Calling (Peak Mode): If provided with peak files (only support two replicates, derived from either 2 true replicates or 2 pseudo-replicates), it performs IDR (Irreproducible Discovery Rate) analysis, filters non-reproducible peaks, and generates a final "conservative" or "optimal" consensus peak set. Trigger this skill when you need to handle more than two replicates (creating pseudo-reps) OR when you need to merge peak lists.
alignment-level-QC
Calculates technical mapping statistics for any aligned BAM file (ChIP or ATAC). It assesses the performance of the aligner itself by generating metrics on read depth, mapping quality, error rates, and read group data using samtools and Picard.Use this skill to check "how well the reads mapped" or to validate BAM formatting/sorting before further processing. Do NOT use this skill for biological signal validation (like checking for peaks or open chromatin) or for filtering/removing reads.
chromatin-state-inference
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.
track-generation
This skill generates normalized BigWig (.bw) tracks (and/or fold-change tracks) from BAM files for ATAC-seq and ChIP-seq visualization. It handles normalization (RPM or fold-change) and Tn5 offset correction automatically. What's more, this skill can help user visualize the signal profiles around TSS or target regions. Use this skill when you have filtered and generated the clean BAM file (e.g. `*.filtered.bam`).
motif-scanning
This skill identifies the locations of known transcription factor (TF) binding motifs within genomic regions such as ChIP-seq or ATAC-seq peaks. It utilizes HOMER to search for specific sequence motifs defined by position-specific scoring matrices (PSSMs) from known motif databases. Use this skill when you need to detect the presence and precise genomic coordinates of known TF binding motifs within experimentally defined regions such as ChIP-seq or ATAC-seq peaks.
differential-tad-analysis
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.
image-gen
Generate images using Gemini via ZenMux
planning
Proactively use when making a plan, e.g. the user says "Let's make a plan".
jj-changelog
Proactively use to generate or update a CHANGELOG.md file from Jujutsu commit history.
jujutsu-planning
Proactively use when planning a complex multi-step implementation.
brainstorming
Proactively use when brainstorming potential solutions to difficult problems.
jira-ticket
Proactively use this skill when you need to read, create, update, or manage Jira tickets.
report-writing
Use this still to write reports.
implement-ticket
Proactively use this skill when implementing a Jira ticket.
SPI Flash Dump via OpenOCD
This skill should be used when the user asks to "dump SPI flash", "read EEPROM through OpenOCD", "dump flash via MCU", "read SPI through debug interface", "extract firmware from SPI", or mentions scenarios involving SPI flash connected to a microcontroller with SWD/JTAG debug access. Provides comprehensive guidance for RAM-resident SPI flash dumping without external programming hardware.
best-practices-extractor
Extract and generate coding best practices from PR review comments. Use when the user asks to "extract best practices", "analyze PR comments", "generate coding standards", "create best practices from PRs", or "update coding guidelines from reviews".
sdk-typescript-patterns
Use this skill when developing TypeScript applications with the Claude Agent SDK (@anthropic-ai/claude-agent-sdk), implementing query() calls, configuring SDK options, handling streaming message iteration, working with SDKMessage and SDKResultMessage types, managing AbortSignal, passing custom env variables, or setting up the single-point-of-contact types file for SDK imports.
sdk-agent-control
Use this skill when controlling agent behavior in TypeScript Agent SDK platforms — restricting allowed tools, setting budget and turn limits, crafting system prompts that guide agents to specific behaviors, implementing the file pre-creation pattern, augmenting prompts with runtime context, building message loggers, or tracking agent run metadata (cost, duration, iterations).
sdk-hooks-development
Use this skill when implementing TypeScript hook callbacks for the Claude Agent SDK — creating PreToolUse hooks to allow/deny tool calls, PostToolUse hooks to inject additionalContext, building factory functions for parameterized hooks, using HookCallback and HookJSONOutput types, applying isPreToolUseInput and isPostToolUseInput type guards, or designing a hooks strategy for an Agent SDK platform. Hooks in the TypeScript SDK are async functions, NOT JSON config files.
gemini
Shell out to Gemini CLI from Claude for any task. Use when asked to "pipe content to Gemini", "get Gemini perspective", "use gemini CLI", "run headless AI task", "parallel analysis with Gemini", or "get second opinion from Gemini". Useful for alternative perspectives, batch processing, or leveraging Gemini 2.5 Pro capabilities alongside Claude.
vsdevshell
Enter the Visual Studio Developer environment in the current PowerShell session via the VsDevShell module (MSBuild/CL toolchain env vars).
plan
Creates detailed implementation plan from validated research. Produces task breakdown with dependencies.
research
Use when needing to understand requirements before implementation. Gathers context from Jira, Confluence, codebase, and docs. Produces research document with confidence scoring.
implement
Executes implementation plan with quality checks and progress tracking. Follows AGENTS.md patterns strictly.
code-review
Code reviewer focusing on correctness, regressions, security, and test coverage - P0/P1/P2 severity
audit-performance
Performance-focused audit that can run in background during implementation. Checks for inefficiencies, memory leaks, widget rebuilds. Injects P0 findings to main agent.
audit-security
Security-focused audit that can run in background during implementation. Checks for vulnerabilities, auth issues, data exposure. Injects P0 findings to main agent.
audit
Validates research/plan/code against overengineering, underengineering, and hallucination
rpi
Use when implementing features from Jira tickets, PRDs, or user requirements. Orchestrates Research-Plan-Implement workflow with quality gates for hallucination, overengineering, and underengineering detection.
agent-mail
Multi-agent coordination via agent-mail CLI. Use when communicating with other agents, coordinating file access, sending/receiving messages, checking inbox, or reserving files. Triggers on "send message to agent", "check inbox", "reserve files", "coordinate with other agents", multi-agent workflows, file reservations, acknowledgements, "list agents", "delete agent", "clean up agents", "purge agents".
hugo-blog
A set of resources to help me write blog posts for hugozhu.site
visualizing-with-mermaid
Create professional Mermaid diagrams with proper styling and visual hierarchy. Use when creating flowcharts, sequence diagrams, state machines, class diagrams, or architecture visualizations.
verification-before-completion
Run verification commands before claiming work is complete or fixed. Use before asserting any task is done, bug is fixed, tests pass, or feature works.
swiftui-expert-skill
Write, review, or improve SwiftUI code following best practices for state management, view composition, performance, modern APIs, Swift concurrency, and iOS 26+ Liquid Glass adoption. Use when building new SwiftUI features, refactoring existing views, reviewing code quality, or adopting modern SwiftUI patterns.
jscodeshift-codemods
Write and debug AST-based codemods using jscodeshift for automated code transformations. Use when creating migrations, API upgrades, pattern standardization, or large-scale refactoring.
systematic-debugging
Four-phase debugging framework with root cause tracing - understand the source before proposing fixes. Use when investigating bugs, errors, unexpected behavior, or failed tests.
index-knowledge
Generate hierarchical AGENTS.md knowledge base for a codebase. Creates root + complexity-scored subdirectory documentation. Use when running /init, onboarding to a new codebase, bootstrapping project documentation, or regenerating stale AGENTS.md files.
eslint-plugin
Author custom ESLint plugins and rules with test-driven development. Supports flat config (ESLint 9+) and legacy formats. Uses @typescript-eslint/rule-tester for testing. Covers problem, suggestion, and layout rules including auto-fixers and type-aware rules. Use when creating or modifying ESLint rules, plugins, custom linting logic, or authoring auto-fixers.
remotion-best-practices
Best practices for Remotion - Video creation in React
refactoring-code
Improve code structure while preserving behavior with test verification. Use when cleaning up code, reducing duplication, simplifying complexity, or reorganizing modules.
beautiful-mermaid
Render Mermaid diagrams as SVG and PNG using the Beautiful Mermaid library. Use when the user asks to render a Mermaid diagram.
slidev
Markdown-based presentation slides powered by Vue and Vite. Use when creating slide decks, technical presentations, conference talks, or any presentation that benefits from code highlighting, diagrams, and web technologies.
ralph-prd
Generate structured prd.json files for autonomous agent loops (Ralph Wiggum pattern). Use when planning bulk/batch tasks, migrations, refactoring campaigns, or any work that can be decomposed into independent items with verification steps.
adversarial-code-review
Review code through hostile perspectives to find bugs, security issues, and unintended consequences the author missed. Use when reviewing PRs, auditing codebases, or before critical deployments.
customizing-opencode
Configure OpenCode via opencode.json, agents, commands, MCP servers, custom tools, plugins, themes, keybinds, and permissions. Use when setting up or modifying OpenCode configuration.
agent-skills
Author and improve Agent Skills following the agentskills.io specification. Use when creating new SKILL.md files, modifying existing skills, reviewing skill quality, or organizing skill directories with proper naming, descriptions, and progressive disclosure.
natural-writing
Write like a human, not a language model. Avoid AI-tell vocabulary, formulaic structures, and hollow emphasis. Apply to ALL written output including prose, documentation, comments, and communication. Use when drafting prose, documentation, comments, or any written output that should sound human.
documenting-code-comments
Standards for writing self-documenting code and best practices for when to write (and avoid) code comments. Use when auditing, cleaning up, or improving inline code documentation.
opensrc
Fetch source code for npm, PyPI, or crates.io packages and GitHub/GitLab repos to provide AI agents with implementation context beyond types and docs. Use when needing to understand how a library works internally, debug dependency issues, or explore package implementations.
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