LLM Mart Basic

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

Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays, organs, cell lines, or targets.

Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs

Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a collection of experiments, manage citations, compare experiments, or track data provenance.

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under

Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact o

Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of E

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Plural alias for task status, pause, prompts, recovery, and ignore

Verify that the autorun plugin command surface is loaded

Tmux session management - create, list, cleanup isolated sessions, short for /ar:tmux

Tmux session management - create, list, cleanup isolated sessions

CLI testing in isolated tmux sessions, short for /ar:ttest

CLI testing in isolated tmux sessions

Graceful stop - finish current task then stop (short for /ar:stop)

Set AutoFile policy to ALLOW — permit creation of new files without justification

Refresh git commit guidelines before staging changes

Set AutoFile policy to FIND — restrict edits to existing files only

Start an autorun task with three-stage verification (initial → critical review → final verification)

Refresh the universal system design philosophy before designing or reviewing code

Show the current AutoFile policy and any active autorun state

Extract text from PDF files or directories to markdown

Trigger: `/ship` or "ship it" or "deploy to production"

Suppress 5-question enforcement for rapid sessions

Check a Dutch address for KPN outages and report what connectivity is available there

Find the KPN business-mobile contract for a lost or stolen phone and block its SIM after confirmation

Run the SkillOpt-Sleep cycle with the handoff backend — no API subprocess; this session answers the engine's model calls via prompt/answer files, in isolated fresh-context subagents

Run or manage the SkillOpt-Sleep self-evolution cycle (review past sessions, replay tasks through a selected backend, consolidate validated memory + skills, or schedule nightly runs)

Your car as a chat-room agent: Raspberry Pi 5 + dashcam + local AI. CodeWatch's sibling for the garage.

The enterprise gateway for autonomous agents. Identity management, per-channel isolation, credential vault, per-session tamper-evident audit log.

AI agent for Home Assistant — talk to your home, create automations in plain language, analyze cameras with face recognition, and get proactive anomaly alerts.…

A desktop app to prototype agent ideas, inspect every harness step, replay failures, and evaluate performance, all in one place. Local-first, cloud-ready for ma…

Local-first AI memory you can see, edit, and override — portable across Claude Code, Codex, Cursor, Windsurf, and other MCP coding tools.

Web & desktop (Electron) client for the OCTO open workplace — one React + TypeScript codebase shipping browser and PC surfaces, with first-class AI agent UX.

同花顺官方 A股金融数据服务，提供股票实时行情、历史行情、财务报表、指数、板块、涨停等数据，适用于 AI Agent、量化研究和应用开发，支持 API、MCP、CLI 和 Python。Official Tonghuashun (HiThink) A-share financial data service provi…

Open-source desktop SQL workspace for PostgreSQL, MySQL/MariaDB, SQLite and 15+ more databases like DuckDB, ClickHouse, Redis and Firestore. Built-in MCP server…

🤖 Local-assist BOSS Zhipin CLI for AI agents — search, welfare filtering, shortlist, JSON-envelope output; low-risk & compliant by default.

The local-first sidebar AI agent for ComfyUI — runs on your own Claude OR ChatGPT subscription (no API keys, no extra LLM costs). Drives your live graph: edits,…

Persistent memory for Claude Code — identity, context, and continuity across sessions

🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…

A curated list of plugins, skills, MCP servers, patch/profile layers, orchestrators & UIs for DeepSeek Harness (DSH). Visualization · PPT · Coding · Agents · Lo…

World Memory Protocol.

Run your own organization of agents.

The most RAM efficient harness

AI-native, free, open-source alternative to Jira, Trello, ClickUp & Monday. Built for Scrum teams where humans and AI agents collaborate as equals — on the same…

Free open-source desktop app that scrapes JAV metadata and generates NFO + cover art for Jellyfin, Emby & Kodi. No Docker, no CLI — one-click install on Windows…

A cross-platform desktop app to manage Agent Skills in one place and sync them to multiple AI coding tools’ global skills directories — “Install once, sync ever…

天枢 (Tianshu) 是一个基于harness工程的终端编程智能体运行时（Tui X Gui），针对DeepSeek V4 做了前缀缓存工程优化（长会话实测稳态命中率 97–99%）和深度适配。它跳出了传统 AI 编程助手把大模型仅当成“工具”的局限，基于认知虚拟机 (CVM)、自感知层和信息素（Stigmergy…