LLM Mart Basic

Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger o

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

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

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.

Get an Ironscales AI verdict on a raw email, then act on it with a remediation action

Triage open Ironscales phishing incidents — list by status and severity, investigate, and remediate

Get a Kaseya Quote Manager quote with its sections and line items

Get a Kaseya Quote Manager sales order with its lines and payments

List Kaseya Quote Manager quotes, optionally scoped to a recent window

Add a note or comment to an existing Autotask ticket

View contract status, entitlements, and remaining hours for a company or specific contract

Check pricing details for an Autotask product or service from price lists

Create a new Autotask quote with line items for products, services, and service bundles

Create a new service ticket in Autotask PSA

Use this skill when working with Autotask expense reports - creating reports, adding expense items, searching by status or submitter, and tracking reimbursable and billable expenses

Search for Autotask configuration items/assets by name, serial number, or company

Search for Autotask companies by name, ID, or other attributes

Search for Autotask contacts by name, email, phone, or company

List tickets currently assigned to you with optional filtering

Reassign a ticket to a different resource or queue

Search the Autotask product catalog for products, services, or inventory items

Search for tickets in Autotask PSA by various criteria

Log time against tickets or projects in Autotask PSA

Update fields on an existing Autotask ticket (status, priority, queue, due date)

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.