LLM Mart Basic

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

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak s

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, o

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.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

{{SKILL_ENTRY:post-merge-cleanup}}

Show the codeArbiter command catalog — the public command list and what each routes to.

{{SKILL_ENTRY:commit-gate}}

Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

{{SKILL_ENTRY:context-check}}

{{SKILL_ENTRY:context-creation}}

{{SKILL_ENTRY:debug}}

{{SKILL_ENTRY:decompose}}

Verify the active host install, package, command ownership, enforcement{{IF:pi}}, wrapper self-test, and active-dispatch coverage gap{{ELSE}}, and harmless live-fire probe{{END}}. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

{{SKILL_ENTRY:finishing-a-development-branch}}

Zero-onboarding, read-only dry-run of the reviewer fleet against the current uncommitted diff. Predicts reviewers, runs the state-free secret scan, writes nothing.

Trim transcript clutter to extend session lifetime — analyze, prune a copy, or toggle the after-each-turn service. Dry-run by default; gains land at resume/compaction, not the current turn.

{{SKILL_ENTRY:decision-variance}}

Open-source super AI assistant & Agent Harness. Plans tasks, runs tools and skills, self-evolves with memory and knowledge. Multi-model, multi-channel. Lightwei…

Open-source AI browser agent for web automation: a web browsing agent and computer-use agent in plain English. Browser MCP for Claude Code and Gemini CLI.

Agent-native trading terminal built on DeepSeek Harness. Crypto, US, CN and HK in one three-column GUI, 19+ hot-swappable connectors, dry-run by default with hu…

Open-source desktop and web coding agent with a first-party host and harness, durable sessions, model connections, streaming chat, and workspace tools.

OrcaReplay — Time travel for AI agents. Record, replay, fork, and debug any agent run with any model. Built by the OrcaRouter.ai team.

A complete toolkit for connecting R and LLMs

OpenSRE — the memory-first AI SRE. Self-hosted incident investigation with episodic memory, knowledge graph, web console, Slack & Teams. opensre.in

A desktop AI coding assistant that works with your local projects. Ally helps you understand code, edit files, search a workspace, manage tasks, and complete de…

【在线免费使用】 简单快速将SQL或DBML转换为美观的ER图（支持 Agent Skill）/ The best SQL to ER Diagram converter (Support Agent Skill).

Operation-bound protection for autonomous AI agents: contain and verify operations before committing changes, understand intent and risk across long-running wor…

Local-first AI coding agent desktop: Electron + Rust host core + pi Agent Harness + user-installable plugins

Local-only Go static analysis engine with a built-in MCP server. Gives AI coding agents deterministic structural awareness: call graphs, impact analysis, symbol…

Self-hosted AI agent workspace with tool calling, MCP, multi-model routing, sandboxed execution, multi-agent workflows, and LLM-authored 3D character animation…

Automated TDD enforcement for Claude Code

High-performance platform for building websites, e-commerce, and web applications—with Native AI, JavaScript development, and a marketplace for portable sites a…

Autonomous AI-agent orchestration engine for job discovery with decision traces, tool adapters, and production-grade run control.

Token efficient Claude Code full Python rebuild. AI Coding Agent in 310K LoC Python.

OPC — One Person Company. A full team in a single Claude Code skill. Adaptive agent orchestrator with 21 built-in roles, 6 flow templates, and adversarial quali…

Open-source, secure environment with real-world tools for enterprise-grade agents.

MCP server for AI-powered GitHub project management — agent orchestration, PRD-to-issues pipeline, sprint planning, and multi-agent swarm coordination