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

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.

Find an organization in IT Glue by name

Retrieve a password from IT Glue (with security logging)

Find a configuration item (asset) in IT Glue by name, hostname, serial number, or IP address

Search IT Glue documentation by keyword or phrase

Get a security posture summary for a RocketCyber customer account

Search RocketCyber security incidents by account, status, severity, verdict, and date range

Locate a Keeper record by description and return its UID and metadata without revealing any credential

Report exactly what the connected Keeper KSM application can reach - folders, record counts, and record types - reading no credential values

Generate a detailed summary of a Liongard environment

Check Liongard connectivity and return system health summary

Audit MFA enrollment across all M365 users, highlighting accounts with no MFA

Look up a Microsoft 365 user by name or email, showing account status, licenses, MFA, and last sign-in

Show Microsoft 365 license inventory - available SKUs, consumed seats, and optimization opportunities

Run the complete M365 offboarding workflow for a departing user - revoke access, handle mailbox, transfer data

Create a Mailprotector block rule for a sender address or domain at a chosen scope

Review the Mailprotector quarantine at any scope and summarize held messages

Onboard a new customer onto Mailprotector - customer, domain, user group, services, users

Release one or more quarantined Mailprotector messages to their recipients

Locate a Meraki device by serial, name, or MAC across an organization's networks

Pull and summarize a Meraki network's L3 firewall rules and flag overly-permissive (any/any allow) rules

Build AI Agents like playing LEGOs. Everything is a Plugin.

The coding agent that answers to you, your model, your machine, your rules.

CI-native agent CLI tool for deterministic pipeline gating.

Local-first cross-platform desktop workspace for Claude Code / agents: multi-agent, Git worktrees, code diffs, skill marketplace, multi-model, Computer Use, tas…

Local-first visual generation runtime and studio for people and coding agents, with reproducible image and video workflows across multiple providers.

A token-efficient MCP server for safe, line-oriented text file editing with partial reads, hash-based conflict detection, and atomic multi-file operations.

Open-source, evidence-driven MCP server for RTL simulation debugging: correlate VCS/Xcelium logs, VCD/FSDB waveforms, SystemVerilog/UVM source, hierarchy, and c…

runs anywhere. uses anything

One macOS app for Claude Code, Codex, and every agent runtime you use — scheduled runs, global hotkey launcher, per-run git worktrees, one review board.

Soul-driven AI agent with permission-hardened tools, token budgets, and multi-channel access. Runs 24/7 from CLI or Telegram.

Email, SMS & phone-call infrastructure for AI agents — send and receive real email and text messages, and place agent-driven outbound voice calls, all programma…

55 MCP tools to drive the Unity Editor from any MCP-compatible AI agent — scenes, GameObjects, prefabs, assets, tests, and builds. OpenClaw gateway included for…

Google Ads MCP + Meta Ads MCP + GA4 in one server for Claude, ChatGPT, Cursor & n8n — 250+ tools, hosted remote MCP, OAuth login, no API keys. By Ryze AI.

Claude Code & Codex 本地 token 追踪 — 状态栏（Codex 业界首创伪 statusline）、GitHub 风格热力图、多模型成本分析。 | Local token tracker for Claude Code & Codex — status line (industry-first…

Empower the Shell to think. Evolve Operations.

🤖 A full-stack Agent Chat Runtime for pre-production validation, built with act, TypeScript, and LangGraph JS combining streaming, multimodal, HITL, and tools…

Cerul — video memory infrastructure for AI products. SDKs, CLI, MCP, and developer integrations.

Stealth headless browser for AI agents — bypass Cloudflare, bot detection, and anti-scraping. Drop-in Puppeteer/Playwright replacement.

Web research for your agents with smart and safe tooling + knowledge store

FuXi is a fast, self-contained AI coding agent that lives in your terminal — edit code, run commands, and drive tools, with cost-aware routing across LLM provid…