LLM Mart Basic

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

Make software health, failure, degradation, and recovery visible through useful observability and diagnostics. Use when adding logs, metrics, traces, health checks, alerts, incident signals, or operational feedback.

Inspect the real repository, environment, dependencies, and runtime evidence before designing or changing software. Use for greenfield construction, unfamiliar codebases, uncertain behavior, or any task where assumptions could create rework.

Reflect on failures, incidents, reviews, and completed software work to turn evidence into durable tests, guardrails, documentation, and process improvements.

Debug software by making failures visible, reproducing them, finding contributing causes, and adding durable regression protection. Use for bugs, failing tests, incidents, regressions, flaky behavior, and unexplained production errors.

Improve software continuously through small, safe, behavior-preserving changes that reduce maintenance cost. Use for refactoring, cleanup, technical debt, naming, duplication, dead code, or post-change polish.

Choose simple, maintainable software designs by removing speculative complexity, comparing alternatives, and making explicit tradeoffs. Use for architecture, API, data-model, dependency, and scope decisions.

Implement software through small, repeatable, integrated vertical slices with clear exit criteria and honest verification. Use when a design is understood and code needs to be built or changed.

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.

This is the only sanctioned way a version tag gets created, and it holds no knowledge of any

A read-only review of the current change, dispatched by path against a reviewer-to-path matrix:

This is the outlet for "I need to write code to find out" rather than "I know what to build." The

This is codeArbiter's autonomy mode. It collapses the usual spec-plan-execute cycle into one

The daily hygiene checklist, made routine and gated: fetch and offer a fast-forward pull, list

A read-only snapshot of `.codearbiter/` state: the project's `stage:` maturity value, every

Wires codeArbiter's renderer into `~/.claude/settings.json`, or removes it. A plugin can't own a

The only blessed way to mutate `.codearbiter/open-tasks.md`. It runs a thin writer over pure

An opt-in, lightweight STRIDE pass over a design before it's built — invoked deliberately, never

Tribunal is codeArbiter's deepest review, for a deliberate audit of a repository or subtree.

Watches a pull request's CI checks to completion without polling by hand. The wait is a real

A fixture command named debug, colliding with the debug skill/agent.

A fixture command named prune, used to regression-test forge badges.

Another command, description only, no argument hint.

A sample command for fixtures — single sanctioned path to a thing.

Convert an animated HTML file (like /fig output) to a perfectly looping high-quality small GIF using Playwright + ffmpeg

Find a free licensed image on the internet and add it to the project, optimized

Art-direction photo pass over the site: add photography only where it earns its place

Audit consolidate or forget stale sensitive or superseded Tree Ring Memory entries

Capture a concise validated lesson decision warning or preference in Tree Ring Memory

Open-source, self-hosted AI media server. One server replaces your entire media stack, with a web app, native iPhone app, and an AI agent that gets things done.…

A curated list of tools built for Jev — TypeSafe AI's System One model for typed decisions.

🦦 Crayotter: A Multimodal AI-Agent for Video-Editing, Video-Composing, and Video Production. Powered by Multimodal LLMs for autonomous Text-to-Video agentic fr…

Webextension tool for Odoo

基于多模态视觉感知与 LLM Agent 的 macOS 微信自动化框架 | Visual RPA for WeChat

The operational superset of Pi Coding Agent — everything Pi, plus observability, governance, recovery, evaluation and multi-agent orchestration. Pi Coding Agent…

Metrik 可以集中查看本机多个 Agent 的配额余量和 Token 消耗，目前支持 ChatGPT、Claude、GLM、Kimi 等主流 AI 服务。

An AI agent with a real self — soul she wrote, desires that drive her, a heartbeat for autonomous action, dreams she processes when you're away. Capability supe…

Production-ready open source terminal coding agent with readable, layered code: permission rules, OS sandboxing, MCP, skills, sub-agents, and Anthropic, OpenAI-…

Answer me with HTML — an agent skill that answers hard questions with a one-page HTML you can actually read. 让 AI Agent 用一页 HTML 回答复杂问题。

Prompt packs that make any AI agent a LaTeX expert — fix errors, polish writing, format for venues, read papers, recover source

Claude Code plugin: universal radial-tree exploration engine. One tree skill + swappable presets (brainstorm / attack / design / code-audit) for divergent ideat…

Claude Code + OpenClaw + Codex + WorkBuddy 中文教程 | 50篇完整教程 + 1张速查卡 | 80万+内容量 | 1500+实操示例 | AI Coding / Agent 四线学习路径（编程+助手+Agent+办公）

SmartLabelBench 2026: LLM-Powered Auto Annotation and Dataset Builder for Everything

从零开始玩转OpenClaw：最全面的中文教程，涵盖安装、配置、实战案例和避坑指南（github版）

Native Android GUI for running AI coding agents locally on-device. No terminal or PC required.

基于 LangChain/LangGraph 的 ReAct Agent ，结合 RAG、工具调用与 Streamlit 界面，面向智能客服与报告生成场景。

An open-source, local-first AI learning workbench

Open-source coding agent for your terminal, built in Rust and on a journey of continuous community improvement. Issues and PRs welcome.

Matt Pocock 技能集的中文翻译版 — 地道中文，原汁原味的技术术语。基于 mattpocock/skills 复刻。每日中午12点钟同步