LLM Mart Basic

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts,

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.

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.

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

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Show the codeArbiter command catalog — the public command list and what each routes to.

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Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

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Verify the active host install, package, command ownership, enforcement{{IF:pi}}, wrapper self-test, and active-dispatch coverage gap{{ELSE}}, and harmless live-fire probe{{END}}. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

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Zero-onboarding, read-only dry-run of the reviewer fleet against the current uncommitted diff. Predicts reviewers, runs the state-free secret scan, writes nothing.

Trim transcript clutter to extend session lifetime — analyze, prune a copy, or toggle the after-each-turn service. Dry-run by default; gains land at resume/compaction, not the current turn.

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AI skill for OpenClaw & Claude Code — recommend from 10000+ Nano Banana Pro (Gemini) image prompts. Smart search by use case, content remix, sample images.

嘉立创EDA专业版(EasyEDA Pro)自动化：给 AI harness 装上画板的「手」—— 一套 typed 原理图/PCB 动作，CLI / Agent Skill / stdio MCP 三形态融合接入。承接嘉立创「不以卖板赚钱，以培养中国工程师为己任」 | EasyEDA Pro automation:…

Claude Code session log viewer for JSONL files in ~/.claude/projects. Browse conversations, tool calls, tokens, and live tail sessions on desktop, web, and TUI.

Shared memory MCP server — persistent, searchable, cross-client Claude, Opencode

OpenAI Codex CLI session log viewer for JSONL files in ~/.codex/sessions. Browse conversations, tool calls, tokens, collaboration chains, and live sessions on d…

High-performance Google Drive CLI and Model Context Protocol (MCP) Server for LLM/AI agents. Natively execute Google Apps Script (GAS) under a secure whiteliste…

"Vibe-Trading: Your Personal Trading Agent"

Local-first chat history analyzer with AI. | 本地优先的 AI 聊天记录分析工具

Official Oxylabs MCP integration

Persistent memory for Claude Code & Codex CLI. Auto-extracted knowledge graph, multi-representation embeddings, 3D WebGL visualization. LongMemEval R@5=97.45%.…

One person, a team of agents. Multi-session CLI that collaborates across terminals; /goal keeps long tasks running; WeChat/WeCom/Feishu gateway lets you call th…

AI 基础知识 - GPU 架构、CUDA 编程、大模型基础及AI Agent 相关知识。

Self-hosted, open-source agent skill registry for enterprises. Publish & version skill packages, govern with RBAC and audit logs, deploy on-premise with Docke…

深度调研报告生成 Skill — 一条命令，十分钟出券商级深度调研报告 / Professional deep research report generation Skill · Supports 19 languages

The OKF toolkit for Claude Code — author, maintain, validate & visualize Open Knowledge Format bundles. Plugin, agent skills, and a GitHub Action.

Autonomous AI pentesting agents — real-time reconnaissance, vulnerability detection, and exploitation orchestration. Go + TypeScript.

Native macOS and iOS App for the Hermes AI agent — multi-window, multi-server (local + remote over SSH). Chat, dashboard, sessions, memory, cron, MCP, and more.

Multiplayer Claude Code and Codex. Self-hosted team workspace for Claude Code and Codex. Multi-user, browser-based, AI mates with memory.

Every past session, subagent, and workflow -- queryable by your agent, browsable by you

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