LLM Mart Basic

Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene e

Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, gen

Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolut

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

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.

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

`crabbox shard` forks a [checkpoint](checkpoint.md) into `--count` leases

`crabbox share` grants other people access to an existing lease through the

`crabbox ssh` resolves a lease and prints a ready-to-run `ssh` command for it.

`crabbox status` prints the current state of a lease: its slug, provider,

`crabbox stop` ends a single lease. For coordinator-backed and direct cloud

`crabbox sync-plan` prints the local sync manifest and its size hotspots

`crabbox tunnel` opens one foreground SSH local port-forward to a resolved

`crabbox unshare` removes sharing rules from a coordinator-backed lease. It is

`crabbox usage` reports lease cost and usage estimates from the broker, broken down by user, organization, or the whole fleet.

`crabbox verify` checks a signed run receipt produced by `crabbox run --attest`.

`crabbox vnc` prints (or opens) the connection details for a desktop-capable

`crabbox warmup` leases a box and waits until it is ready: it provisions (or

`crabbox watch` runs a command on a warm lease, then watches the local

Linux portal viewers default to **Match window**: only the connected controller

`crabbox whoami` calls the broker's `/v1/whoami` endpoint and prints the

Vet a new or changed third-party dependency for license, provenance, and supply-chain risk before any install runs.

Report the health of Architecture Decision Records — aged, unchallenged, supersession candidates, unresolved CONFIRM-NN. Read-only.

Author a numbered, dated, user-attributed Architecture Decision Record under .codearbiter/decisions/.

Assemble the governance record for a range — commits, overrides, ADRs, sprint auto-decisions, open questions, checkpoint findings — into one dated audit packet. Read-only.

Lightweight Q&A about the project — answer from context and return, no routing, no state change.

A systematic AI Agent development tutorial covering LLM agents, RAG, tool use, memory systems, multi-agent systems, LangChain, LangGraph, MCP, and agentic RL.｜从…

Convert Files / Folders / GitHub Repos Into AI / LLM-ready Files

Open-source, local-first conversational AI video editor with a professional multi-track timeline, Agent Skills, MCP integration, and Remotion rendering.

Maintainer-governed agent for evidence-backed open-source contribution proposals

A Claude Code skill by Hao (駱君昊) that learns your Facebook voice and auto-posts to FB / IG / Threads / X with a 14-day content calendar. Mega-viral validated: 8…

Local-first AI agent workspace for coding, writing, design, research, and automation — one runtime for desktop GUI and TUI.

Open-source AI Agent platform for teams. Your agents don't just chat — they read files, run code, call APIs, and deliver results.

Give your AI agent eyes for PDFs — structured text, tables, OCR, visual evidence, and page-level citations via MCP. Native Rust, local-first.

Real-world AI penetration testing engineer for authorized assessments — built-in cloud module covering AWS/Azure/GCP + Aliyun/Tencent/Huawei clouds. Built on Cl…

OpenGUI is an Android GUI agent framework for phone-use AI that can see, plan, and operate real mobile apps through the GUI.

Tinybot is a lightweight personal AI Agent that is constantly evolving

Goink 桌面 AI 小说创作助手，对话式写作 + 自动状态追踪 + 本地语义搜索。跨平台开箱即用。AI Agent Novel Generator.

Pluggable DeepSeek-colored TUI for DeepSeek Harness

Entity-level git merge driver. Resolves false conflicts git invents when independent agents edit the same file. ~95% reduction vs. line-based merge.

Percho: Minimalist desktop GUI for the Pi coding agent — the same engine as the Pi CLI, in a clean visual interface. Multi-session chat, visual tool approvals,…

Run Claude Code, Codex & Gemini in parallel on Windows & macOS — git worktree fan-out with atomic hunk adoption, approval gates, reboot-surviving sessions

A hierarchical memory framework for personalized presentation agents. Try it at memslides.com.

Real-time multimodal desktop agent evolving toward a persistent AI OS interface (0.1 α).

clawdcursor compiles whatever's on screen into one UI map — accessibility tree and OCR fused into stable, addressable elements, with a screenshot only when need…

Repeatable agentic engineering. The workflow layer that turns AI coding agents into a disciplined factory: durable specs, fresh-context workers, adversarial cro…