LLM Mart Basic

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

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,

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.

Generate ranked improvement ideas by scanning the codebase, divergent ideation, adversarial critique, and impact ranking

Full autonomous engineering workflow (plan, build, review, ship)

Transform feature descriptions into well-structured project plans following conventions

Report a bug in the whetstone plugin

Reproduce a GitHub issue bug with visual evidence (browser screenshots, log analysis). Takes a GitHub issue number. For non-issue bug validation, use the bug-reproduction-validator agent.

Resolve PR review comments with cluster analysis and parallel agents. Use when bulk-fixing PR comments after triage.

Perform exhaustive code reviews using multi-agent analysis, ultra-thinking, and worktrees

Diagnose the whetstone environment and configure review agents. Checks CLI dependencies and plugin version, then runs the review-agent wizard that writes whetstone.local.md. Use when onboarding a project, troubleshooting missing tools, or configuring review agents.

Run browser tests on pages affected by current PR or branch

Run pre-PR verification chain: build, types, lint, tests, security scan, diff review

Execute work plans efficiently while maintaining quality and finishing features

Run a dry run first:

Run:

Run:

Create or update an OpenCode skill using the bundled skill-creator workflow

Rebuild the OpenCode skill registry for the current project and installed skills

Session-2 fix loop for Agentation — read structured annotations from the dev overlay and apply targeted UI fixes.

Consume the project's design contract — a .design file or DESIGN.md — and thread its tokens through UI code (CSS, Tailwind, or design-system components).

Fork pov.md for installer taste, or append a one-liner to gotchas.md after a real agent failure.

Audit animation timing, easing, springs, and transitions — decide first whether motion should exist, then apply the motion cluster.

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