nested-TAD-detection
This skill detects hierarchical (nested) TAD structures from Hi-C contact maps (in .cool or mcool format) using OnTAD, starting from multi-resolution .mcool files. It extracts a user-specified chromosome and resolution, converts the data to a dense matrix, runs OnTAD, and organizes TAD calls and logs for downstream 3D genome analysis.
TF-differential-binding
The TF-differential-binding pipeline performs differential transcription factor (TF) binding analysis from ChIP-seq datasets (TF peaks) using the DiffBind package in R. It identifies genomic regions where TF binding intensity significantly differs between experimental conditions (e.g., treatment vs. control, mutant vs. wild-type). Use the TF-differential-binding pipeline when you need to analyze the different function of the same TF across two or more biological conditions, cell types, or treatments using ChIP-seq data or TF binding peaks. This pipeline is ideal for studying regulatory mechanisms that underlie transcriptional differences or epigenetic responses to perturbations.
differential-region-analysis
The differential-region-analysis pipeline identifies genomic regions exhibiting significant differences in signal intensity between experimental conditions using a count-based framework and DESeq2. It supports detection of both differentially accessible regions (DARs) from open-chromatin assays (e.g., ATAC-seq, DNase-seq) and differential transcription factor (TF) binding regions from TF-centric assays (e.g., ChIP-seq, CUT&RUN, CUT&Tag). The pipeline can start from aligned BAM files or a precomputed count matrix and is suitable whenever genomic signal can be summarized as read counts per region.
ChIPseq-QC
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.
ATACseq-QC
Performs ATAC-specific biological validation. It calculates metrics unique to chromatin accessibility assays, such as TSS enrichment scores and fragment size distributions (nucleosome banding patterns). Use this skill when you have filtered BAM file and have called peak for the file. Do NOT use this skill for ChIP-seq data or general alignment statistics.
loop-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.
integrative-DMR-DEG
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration workflows, using promoter-level methylation–expression relationships.
peak-calling
Perform peak calling for ChIP-seq or ATAC-seq data using MACS3, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
hic-compartment-shift
This skill performs A/B compartment shift analysis between two Hi-C samples.
global-methylation-profile
This skill performs genome-wide DNA methylation profiling. It supports single-sample and multi-sample workflows to compute methylation density distributions, genomic feature distribution of the methylation profile, and sample-level clustering/PCA. Use it when you want to systematically characterize global methylation patterns from WGBS or similar per-CpG methylation call files.
methylation-variability-analysis
This skill provides a complete and streamlined workflow for performing methylation variability and epigenetic heterogeneity analysis from whole-genome bisulfite sequencing (WGBS) data. It is designed for researchers who want to quantify CpG-level variability across biological samples or conditions, identify highly variable CpGs (HVCs), and explore epigenetic heterogeneity.
correlation-methylation-epiFeatures
This skill provides a complete pipeline for integrating CpG methylation data with chromatin features such as ATAC-seq signal, H3K27ac, H3K4me3, or other histone marks/TF signals.
atac-footprinting
This skill performs transcription factor (TF) footprint analysis using TOBIAS on ATAC-seq data. It corrects Tn5 sequence bias, quantifies TF occupancy at motif sites, generates footprint scores, and optionally compares differential TF binding across conditions.
regulatory-community-analysis-ChIA-PET
This skill performs protein-mediated regulatory community analysis from ChIA-PET datasets and provide a way for visualizing the communities. Use this skill when you have a annotated peak file (in BED format) from ChIA-PET experiment and you want to identify the protein-mediated regulatory community according to the BED and BEDPE file from ChIA-PET.
image-gen
Generate images using Gemini via ZenMux
implement-ticket
Proactively use this skill when implementing a Jira ticket.
brainstorming
Proactively use when brainstorming potential solutions to difficult problems.
jujutsu-planning
Proactively use when planning a complex multi-step implementation.
planning
Proactively use when making a plan, e.g. the user says "Let's make a plan".
report-writing
Use this still to write reports.
jira-ticket
Proactively use this skill when you need to read, create, update, or manage Jira tickets.
jj-changelog
Proactively use to generate or update a CHANGELOG.md file from Jujutsu commit history.
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-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.
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-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.
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).
audit
Validates research/plan/code against overengineering, underengineering, and hallucination
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.
code-review
Code reviewer focusing on correctness, regressions, security, and test coverage - P0/P1/P2 severity
implement
Executes implementation plan with quality checks and progress tracking. Follows AGENTS.md patterns strictly.
research
Use when needing to understand requirements before implementation. Gathers context from Jira, Confluence, codebase, and docs. Produces research document with confidence scoring.
plan
Creates detailed implementation plan from validated research. Produces task breakdown with dependencies.
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
refactoring-code
Improve code structure while preserving behavior with test verification. Use when cleaning up code, reducing duplication, simplifying complexity, or reorganizing modules.
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.
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.
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.
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.
remotion-best-practices
Best practices for Remotion - Video creation in React
writing-tests
Write behavior-focused tests following Testing Trophy model with real dependencies, avoiding common anti-patterns like testing mocks and polluting production code. Use when writing new tests, reviewing test quality, or improving test coverage.
xcodebuildmcp
Official skill for XcodeBuildMCP. Use when doing iOS/macOS/watchOS/tvOS/visionOS work (build, test, run, debug, log, UI automation).
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.
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.
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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