hic-matrix-qc
This skill performs standardized quality control (QC) on Hi-C contact matrices stored in .mcool or .cool format. It computes coverage and cis/trans ratios, distance-dependent contact decay (P(s) curves), coverage uniformity, and replicate correlation at a chosen resolution using cooler and cooltools. Use it to assess whether Hi-C data are of sufficient quality for downstream analyses such as TAD calling, loop detection, and compartment analysis.
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.
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.
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.
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.
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.
requirement-analysis
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writing-plans
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using-git-worktrees
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quick-fix
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test-driven-development
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exploring
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executing-plans
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anysearch
Real-time search engine supporting web search, vertical domain search, parallel batch search, and URL content extraction.
visual-preview
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acceptance-qa
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zotero-search
Search the user's local Zotero library, find related papers via Semantic Scholar, and discover citations/references. **Claude Code only** - this skill requires a local Zotero instance and access to a port on localhost. Use when the user asks to search their Zotero library, find papers on a topic, explore citations of a paper, or find related literature. Supports cross-referencing Semantic Scholar results against the local library.
thinking-frameworks
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quarterly-connect
Assist users in creating quarterly connects that act as a strategic partner to guide employees through comprehensive quarterly reflections, helping craft insightful narratives for Quarterly Connection reviews that align with company values and career development goals.
template-slide-deck
Generate professional slide decks using company-provided template presentations. Use this skill when the user wants to create a presentation based on their own branded PowerPoint template, company slide deck template, or organizational design standards. Triggers include requests like "create slides using our template", "make a presentation with our company format", "generate a deck from this template", or "build slides matching our brand". Also use when the user asks to create slides and has uploaded or mentioned a template .pptx file.
brainstorming
Use when creating or developing anything, before writing code or implementation plans - refines rough ideas into fully-formed designs through structured Socratic questioning, alternative exploration, and incremental validation. Optimized for git worktree workflows and Claude CLI agent patterns.
resume-builder
Generate beautiful, professionally designed resumes as 1-2 page PDFs. Creates clean, sophisticated layouts that balance visual appeal with readability, tailored to specific job opportunities when provided.
family-menu
Use when users want to plan family dinners, build a weekly meal plan, generate a refrigerator-ready menu PDF, organize a week's grocery shopping around dinner, or kick off a meal-prep week with recipes and a shopping list.
autoclaude-task-converter
Convert single-file task backlogs (TASKS.md format) to AutoClaude multi-file spec structure. Use when the user wants to (1) convert existing TASKS.md or similar task backlog files to AutoClaude specs, (2) initialize a new project with AutoClaude-compatible task structure, (3) migrate task definitions from simple markdown to the multi-file spec format with requirements.json, context.json, implementation_plan.json. Triggers on phrases like "convert tasks to AutoClaude", "set up AutoClaude specs", "migrate backlog", "create spec from task".
datasette-plugins
Writing Datasette plugins using Python and the pluggy plugin system. Use when Claude needs to: (1) Create a new Datasette plugin, (2) Implement plugin hooks like prepare_connection, register_routes, render_cell, etc., (3) Add custom SQL functions, (4) Create custom output renderers, (5) Add authentication or permissions logic, (6) Extend Datasette's UI with menus, actions, or templates, (7) Package a plugin for distribution on PyPI
skill-creator
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.
agenticflow-skills
ALWAYS use this skill when the user mentions AgenticFlow, AF CLI, AI agents, agent workflows, business packs, workforce orchestration, or wants to create/deploy/run AI agents. Also use when the user wants to set up, build, or automate a business with agents — including tutoring, freelance, Amazon seller, marketing, sales, support, content, coaching, consulting, legal, real-estate, or any domain-specific agent team. Provides CLI commands, pack recommendations, and deployment guides.
gemini-image-generator
Generate images using Google Gemini with customizable options
extreme-code-quality-review
Run an extremely strict maintainability review for abstraction quality, giant files, and spaghetti-condition growth. Use for an extreme code quality review, deep code quality audit, or especially harsh maintainability review.
serverless-aws
Patterns for AWS Lambda, DynamoDB, SQS, and Secrets Manager. Use when working on serverless AWS projects.
writing-style
Write in Steven's voice—pragmatic, curious, pedagogical. Opens with measurable payoffs, builds mental models from first principles, uses worked examples, and handles uncertainty honestly. Use for essays, blog posts, and technical articles.
rifts
Backward-compatible alias for speedrift. Use this when users say "rifts"; apply the speedrift Workgraph autopilot workflow and commands.
recover-after-reboot
Use when asked to recover after a reboot, restart, OS update, lost tmux sessions, dead Codex agents, reboot-backup restore, tmux relaunch, corrupt git index repair, or stranded local commits from pre-reboot agents.
prospecting-partner
Use when researching, qualifying, segmenting, prioritizing, or preparing target lists for prospects, partners, investors, BD contacts, customers, advisors, or outreach campaigns.
obsidian-vault-intelligence
Use only when explicitly working with the legacy Obsidian vault or Obsidian MCP. Folio is the default personal knowledge system; this skill is for legacy Obsidian access, migration, or debugging.
model-mediated-development
Use when designing or building systems with AI/model calls, model-facing APIs, MCPs, CLIs, semantic routing, model memory, agent workflows, tool use, or model-owned decisions where coding agents might add rules, heuristics, regexes, thresholds, fallbacks, or hidden deterministic judgment.
linear
Use when managing Linear issues, creating tasks from conversations, tracking work items, or querying project status - provides bash scripts to interact with Linear's GraphQL API without writing queries directly (project, gitignored)
keynote-slides
Build Keynote-style single-file HTML slide decks with brand-ready templates, minimal navigation, and Gemini nano banana media generation. Includes Narrative Engine integration for framework-driven deck creation with 17 proven storytelling structures and 5-agent review panel. Use when creating or editing slide decks, transforming content into presentations, or generating slide visuals.
github-integration
Use when creating GitHub issues, managing PRs, updating issue states, or searching repositories - provides bash scripts to interact with GitHub REST API without writing API calls directly
gemini-cli-extension-porting
Use when porting beads or superpowers workflows into Gemini CLI extensions or designing Gemini CLI command prompts that emulate multi-step agent workflows - covers extension layout, GEMINI.md context, command TOML patterns, and enforceable guardrails (tests/CI/pre-commit)
orchestrating-tmux-claudes
Orchestrate multiple AI instances (clauded/codex CLIs) in tmux panes. Self-discovering coordinator with mandatory verification, synchronous monitoring, and auto-approval. Zero hallucination via imperative commands. (project, gitignored)
paia-workboard
Use when working with the user's PAIA workboard, paia-work tasks, Workgraph-backed personal task boards, agent task handoff, task status, task creation, claiming, completion, comments, or planning work from the PAIA board.
perplexity-research
Use when conducting web research with Perplexity API - covers authentication, search strategies, structured output generation, and integration patterns for Claude-interpretable results
pi-privileged-execution
Use when a local Pi agent needs administrator privileges, a password-protected command, or approval for global or ambiguous deletion
planforge
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google-docs-automation
Use when agents need Google Workspace access across Drive, Docs, Sheets, Calendar, Slides, Tasks, People, or related GWS services; choose the correct gws-account profile before using gws CLI or domain-specific gws-* skills. Do not use Python gspread/googleapiclient or custom OAuth. Use msgvault for email search/reading.
reminders-management
Use when managing Apple Reminders via MCP - covers list organization, reminder creation/updates, search patterns, and integration with other productivity workflows
roborev-address
Use when a user asks to address or close a specific roborev code review job after fixing or responding to findings.
webwright
Use when the user needs to automate a real web task through a browser — filling forms, applying filters, extracting data, clicking through multi-step flows, or building reusable web automation scripts. Use when a task requires interacting with a live website where the agent must navigate, select, verify, and capture evidence. Do NOT use for API calls, static scraping, or tasks that don't need a real browser.
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