LLM Mart Basic

Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal cor

Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif datab

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is DNA methylated/unmethylated in my tissue?" by combining per-CpG methylation data

Guide for de novo and known motif enrichment analysis of ENCODE ChIP-seq and ATAC-seq peaks using HOMER and MEME Suite. Use when users need to discover TF binding motifs in peaks, validate ChIP-seq targets, or find co-binding partners. Trigger on: motif analysis, HOMER, MEME, de

Integrate multiple ENCODE data types (RNA-seq, ATAC-seq, Histone ChIP-seq, TF ChIP-seq) for a tissue/cell type to build a comprehensive regulatory landscape. Use when the user wants to answer "what are the enhancers, promoters, and regulatory elements active in my tissue, and whi

Guide for annotating ENCODE peaks with genomic features using ChIPseeker and GREAT. Use when users need to assign peaks to genes, determine genomic feature distribution (promoter, intron, intergenic), or perform gene ontology enrichment of peak-associated genes. Trigger on: peak

Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosom

Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak ca

Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pip

Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing DNase-seq data, calling DNase hypersensitive sites, performing footprinting analysis. Trigger on: DN

Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing Hi-C data, generating contact matrices, or calling loops. Trigger on: Hi-C pipeline, chromatin co

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression

Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing WGBS/bisulfite-seq data, calling methylation levels, generating bedMethyl f

Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks

Evaluate ENCODE experiment quality using standard metrics and audit flags. Use when the user asks about data quality, wants to filter for high-quality experiments, needs to interpret quality metrics (FRiP, NSC, RSC, NRF, IDR, TSS enrichment, fragment size), wants to understand EN

Discover and characterize regulatory elements (enhancers, promoters, silencers, insulators, super-enhancers) using ENCODE data and the cCRE catalog. Use when the user wants to find candidate regulatory elements, identify active enhancers in a tissue, map promoter states, classify

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods,

Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq dat

A green PR, a controller reporting success, and not one line of the new code running

Discover testnet↔mainnet subnet lineage from repo configs and open a PR for review (pass --dry-run to report only)

Triage raw inbox notes into reviewed repository destinations without deleting their sources.

Audit and rewrite content to remove AI writing patterns

Log a completed piece of content to content/log.md after the user confirms it was published.

Validate a dream artifact, review each proposal, and apply only individually accepted changes.

Run a curator pass against the validated memory directory and produce a proposal artifact.

End a session — log what happened, update state and the decision log, propose memory updates, and check for uncommitted or unpushed work

Find relevant context files by topic. Use when you need to load files for a topic without a slash command, or when a task spans multiple domains.

Inventory and migrate selected Gemini CLI workflows with dry-run review and parity checks.

Find repeated workflows in selected Gemini CLI sessions and draft portable skills after review.

Scan multi-session drift and offer individually reviewed fixes only after explicit approval.

Scan orphaned worktrees and stale branches, then offer explicit approval-gated cleanup.

Guided onboarding or import for durable workspace context

Start a session — load state files, flag staleness, and give a briefing on current priorities, deadlines, and blockers

Create a morning heartbeat from repository state and update the local heartbeat log.

Mid-session checkpoint — append progress to today's session log and update state files if a priority shifted, without ending the session

Maintainer-only. Find every file that would newly ship to adopters, classify each one against the written distribution-boundary categories, default to withhold on no clean match, and ask the maintainer only where the taxonomy does not settle it. Drives the release CLI, which refuses to produce a manifest until every shipping file has an answer.

Audit memory, wiki, and auto-loaded files for duplication, conflicting instructions, and stale content. The default path researches, then asks you a single Apply / Discuss / Decline question; on Apply it applies the report, files any out-of-scope problem as a tech-debt issue, then commits, opens a PR, and merges it on a main-branch run like /update-deps. Pass --apply to re-run the apply-and-publish stage against the most recent report.

Fix the tech-debt backlog, a single issue or a recommended related batch, highest severity then oldest first, on a fresh isolated branch through the audit gate, closing the issue(s) on merge. Pass `list` to see the ordered backlog, `why <issue-number>` to explain the recommendation, or a bare `<issue-number>` to fix that issue directly.

Health-check and auto-heal this project's Claude integration, triage, heal, verify, and report an F-to-A+ grade.

🤖 MateClaw — Your second brain with Multi-Agent Orchestration, MCP Protocol, Skills & Memory, Dream, and Multi-Channel Support. Built on Spring AI Alibaba.

Vibe-Research: Your Personal Trading Research Agent · A股/美股/港股 的个人投研 Agent：每日复盘、资讯雷达、个股数据、板块中心、我的持仓、研究记录、回测。Vibe-Research 把数据和功能配齐，由你自己的 Agent 驱动投资研究。基于开源的 Code…

Wayland - The AI Agent That Perceives. Reasons. Acts. Evolves.

Observability and enforcement for AI agent harnesses. Capture every run and runtime reliability with policy enforcement. 40 built-in policies, a local dashboar…

Turn your Solana Seeker (or any Android phone) into a 24/7 personal AI agent

A curated collection of offensive, defensive and AI/LLM security tools.

AI agent 通用任务治理框架：对齐目标与事实，规划和调度能力，守住授权与风险边界，治理任务执行到真实验收与交付。Governance framework for evidence-driven planning, orchestration, and verified delivery.

Open-source (Apache-2.0) PDF takeoff for construction & flooring — the first engine an AI agent drives natively over MCP, not bolted on. One-click room detectio…

Stop degrading your model's reasoning. A minimal, zero-config AI coding agent. Enforced ephemeral subagents keep context pure. From tiny local models up to Sol,…

实习.skill — 双非也能拿大厂 offer。帮你改简历、抠面经、准备面试，把真实背景翻译成面试官想要的样子。

专门为 agent 打造的 agent 搜索工具，具备多语言搜索能力，覆盖中文/英文/学术/代码/购物/金融/新闻/百科。

Local-first AI agent workspace for multi-agent collaboration, agent orchestration, scoped permissions, evidence-aware runs, and human-in-the-loop decisions.

Keyboard-first desktop Kanban workspace for AI coding agents with embedded terminals, git worktrees, and hook-driven task tracking.

Claude Code Prompt Mechanism Visualizer — Electron desktop app

Multi-repo semantic code search MCP server in Rust — hybrid vector + BM25 retrieval, tree-sitter AST chunking, fully offline. For OpenCode, Claude Code, Cursor,…

One-ink editorial print image skill — warm paper, halftone photography, active negative space, and restrained typography.

US stock market data for AI coding assistants — zero-auth, official sources. CBOE options with full Greeks + 0DTE flow, FINRA market-wide short volume, SEC EDGA…

AI-powered Werewolf (Mafia) social deduction game where every player is controlled by top LLMs like DeepSeek, Qwen, Gemini, and more

A股全栈数据工具包 · 十一层架构 · 54端点 · 19数据源 · 零鉴权 | Full-stack China A-share data toolkit for AI agents — 11 layers, 54 endpoints, 19 sources, zero-auth

Agentic desktop GUI client for Elasticsearch, OpenSearch, DynamoDB, MongoDB & EasySearch. Natural language queries, visual management, and monitoring. Privacy-f…