LLM Mart Basic

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

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

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.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

Treat an AI agent skill as both an instruction package and a software dependency: inspect what it says, what it runs, what it can access, and how it updates.

`crabbox inspect` prints the full record for a single lease: state, provider,

Run named, repo-local jobs defined in your Crabbox config.

`crabbox list` shows the current Crabbox machines (leases) for a provider. It is

`crabbox login` authenticates the CLI against a coordinator, stores the

`crabbox logout` clears the stored broker token from your user config so the CLI

`crabbox logs` prints the retained command output for a recorded run.

`crabbox marketplace` previews the Crabbox credits gateway: one Crabbox billing

`crabbox media` turns a recorded desktop video into lightweight review

`crabbox open` prepares an existing SSH-capable lease for an external editor.

`crabbox pause` pauses a single lease, freeing the remote compute while

`crabbox pond` is the cross-provider peer-discovery and lifecycle surface for a

`crabbox pool` contains machine-pool helpers. `pool list` keeps the older

`crabbox ports` bridges provider-native port publishing for an existing Crabbox

`crabbox prewarm` leases a reusable box and prepares it for test runs. For

`crabbox providers` prints the provider capability matrix that the CLI compiles

`crabbox receipt <run-id>` retrieves a brokered run's committed terminal

`crabbox results` prints the structured test summary attached to a recorded

`crabbox resume` resumes a lease previously paused with [`pause`](pause.md),

`crabbox run` syncs the current dirty checkout to a box, runs a command there,

`crabbox screenshot` captures a single PNG from a desktop lease without opening a

An open-source, privacy-first, self-hosted knowledge workspace where humans and AI agents work together 开源、隐私优先、自托管的知识工作空间，让人与智能体在此协作

Scale computer-use 2.0 with open-source drivers, cross-OS fleets, and benchmarks for training, evaluation, and data generation.

The go-to web for your AI coding agent — local-first search, fetch, crawl & research over MCP. No API keys, no cloud, $0/query. Public beta.

Transform and optimize your markdown documentation for Large Language Models (LLMs) and RAG systems. Generate llms.txt automatically.

合乎周礼：DeepSeek-powered Zhouli-style Chinese translator, web app, and distributable Skill package.

This is a fork of the https://dockbox.dev project I made

🏆 Curated, ranked list of AI agent harnesses (100+) — plus an MCP server, llms.txt & JSON so agents can recommend them too. Rescored weekly.

A Python framework for modular, self-contained skill management for machines.

ADHD — a skill for coding agents. Tree-of-thought with pruning, built on the Claude & Codex Agent SDK. Fans out parallel divergent thoughts under different cogn…

AI Agent 驱动的开源可自部署视频工作台：将小说与剧本转为角色、场景、道具资产、分镜、视频和剪映草稿，支持跨镜头一致性、多供应商与费用追踪 | Self-hosted AI video workspace for stories, storyboards and short-form video producti…

DeepSeek Harness Desktop App: a local AI desktop workspace for DSH Sessions, projects, files, web research, plugins, and Office artifacts.

Autonomous Offensive Security, Bug Bounty & Red Teaming Agent Framework powered by Hermes Agent, specialized reasoning skills, and multi-model LLM orchestration…

⌥ Coding agent with the IDE wired in

Supercharge AI Agents, Safely

X (Twitter) Scraper API and X API Alternative. You do not need an official X developer account. You do not need to connect or use an X account for supported scr…

My AI Stand. Realtime by day, rewriting itself by night. Summon my AI superpower.

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

观澜 / Guanlan：AI Agent 的中文互联网研究、阅读与信源路由工具。

Mac Agent for macOS 26: the agentic AI harness for your Mac Desktop. Computer use, automation, scripting, coding, and more. Powered by 18+ providers across loca…

Semantic version control => entity-level diffs, blame, and impact analysis on top of git. 28 languages via tree-sitter. Built for coding agents.