LLM Mart Basic

Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinica

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

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

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.

Search Clio contacts by name, company, or email

Search or list Clio matters by name/client and status

Capacity forecast for cloud resources, scoped to a resource type or covering everything connected

Cloud cost anomaly and reclaimable-spend report for a given window

Full network health sweep across all connected network-monitoring tools — devices down, degraded links, and topology changes

Report control and configuration drift since the last known-good baseline for a client or the whole portfolio

Build a source-cited compliance evidence package for a client against a named framework

Draft evidence-backed answers to the standard cyber-insurance questionnaire for a client

List computers in ConnectWise Automate with optional filters

Execute a script on an endpoint in ConnectWise Automate

Create a ConnectWise CPQ quote by copying a template or an existing quote

Get a ConnectWise CPQ quote with its tabs, line items, customers, and terms

List ConnectWise CPQ quote templates available to copy

Search ConnectWise CPQ quotes by account, status, or date range

Add an internal or external note to a ConnectWise PSA ticket

View agreement status and entitlements for a company in ConnectWise PSA

Close a ConnectWise PSA ticket with resolution notes

Create a new service ticket in ConnectWise PSA

Retrieve detailed ticket information from ConnectWise PSA

Log a time entry against a ConnectWise PSA ticket

面向中文开发者的 Claude Code Skills / Agents / Plugins 精选与原创技能库｜按场景分类｜复制即装｜持续更新

原生 macOS Git 客户端，以 Agent 驱动仓库管理、审阅与协作。

A 股短线复盘看板：涨停池·连板梯队·龙虎榜·板块资金一屏看完，赚钱效应/晋级率/梯队断层/情绪周期等派生指标纯计算直出（不经过 AI），AI 只把数据串成能读的盘面研判。全本地运行，可用 Claude/Codex 订阅免 API key。| A-share short-term daily-review dashbo…

禁漫天堂 Agent Skills / AI 原生 JMComic 助手：通过 MCP 与 Skills 将 JMComic 注入你的 AI Agent. / AI-powered JMComic assistant for seamless integration with AI Agents via MCP & S…

Pairlet (formerly CC Pocket / cc-pocket) — Continue your local AI coding tasks from phone, tablet, or desktop.

Self-hosted Personal AI + agent runtime in .NET (NativeAOT-friendly)

A self-hosted knowledge platform for humans and AI agents — publish wikis, blogs, and portable Agent Skills.

Notion CLI with AI agent support. Smart queries, Obsidian sync, batch ops, backups, validation and more.

AI Coding Agent Multiplexer

Independent executor–verifier orchestration for software changes.

AI-native, local-first video editor by Ribbi — runs entirely in the browser. Rust/WASM engine, WebGPU compositing, WebCodecs export; humans and LLM agents edit…

Distill your knowledge, memories, and decisions into an open-source, inspectable AI Agent Twin.

🔬 Harness Vibe Research with Self-evolving AI Scientists

Personal AI desktop agent for Windows, macOS, Linux, Android & iOS. Set a goal, it works on its own. Teams (pair two desktops, agents + humans), Agent2Agent, Wo…

Run agents like a company. AgentOS is the native control plane for OpenClaw — manage agents, tasks, models, context, approvals, and runtime visibility from one…

Create Agentic admin panels faster on TypeScript and Vue.js with AdminForth Framework. Setup main CRUD pages within minutes, extend as you need

OpenJudge: A Unified Framework for Holistic Evaluation and Quality Rewards

An ebook reader with a self-evolving agent: it remembers your reading across books, and plugins extend the reader and the agent alike.

A curated list of awesome resources for vibe coding

Agentic Voice Notes for iPhone and macOS - Rust, Dioxus, LanceDB + RIG + SQLite