LLM Mart Basic

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,

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.

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.

Analyze git diffs or staged changes and generate conventional commit messages that explain WHY a change was made. Supports auto-detecting type and scope, intelligent file staging, and interactive overrides. Use when asked to "write a commit message", "generate a commit", "describe my changes", "commit this", "summarize my diff", or "/commit".

SOC 2 compliance for Terraform — gap analysis, control implementation, evidence collection, and remediation guidance mapped to SOC 2 Trust Services Criteria.

Generate, review, secure, and test composite GitHub Actions following best practices — full repo scaffold, interview-driven generation, PR creation on existing repos, SHA pinning, secrets-as-inputs, job summaries, and actionlint validation.

Set up and troubleshoot Datadog — Agent deployment on Kubernetes, APM instrumentation, Log Management, Monitors, Dashboards, SLOs, Synthetic tests, and live incident investigation using the Datadog MCP server. Covers Terraform-managed Datadog resources.

Structured platform troubleshooting — classifies the problem layer, collects evidence, forms a root-cause hypothesis, and proposes a fix with validation and rollback steps.

Generate, format, and validate code documentation — docstrings, JSDoc, OpenAPI/Swagger specs, documentation sites, and developer guides.

Measure, benchmark, instrument, and debug DORA metrics (Deployment Frequency, Lead Time for Changes, Change Failure Rate, MTTR) for production engineering teams. Covers GitHub Actions instrumentation, Prometheus recording rules, Grafana dashboards, incident source integration, SaaS tool selection, and anti-pattern detection. Use when asked to "instrument DORA metrics", "benchmark our deployment frequency", "why is my MTTR data missing", or "generate a DORA dashboard".

Deploy and configure Dynatrace — OneAgent Kubernetes Operator, code-level instrumentation, Log Monitoring, custom metrics, SLOs, Dashboards, anomaly detection, Davis AI, and live incident investigation using the Dynatrace MCP server. Covers Terraform-managed Dynatrace resources.

FluxCD entry point — routes to the right workflow based on what you need. Live cluster issue → structured 5-workflow debug trace. Repo health check → 6-phase audit (discovery, validation, API compliance, best practices, security). Helm chart review → helmchart. Starts by asking one question to confirm the right mode.

Design, review, secure, and debug GitHub Actions workflows — reusable workflows, OIDC federation, SHA pinning, token scoping, promotion orchestration, and CI failure diagnosis.

Flux CD and Argo CD — two modes. debug: five structured debug workflows for live clusters (installation, source, HelmRelease, Kustomization, ResourceSet) producing a five-section report. audit: six-phase read-only repo analysis (discovery, validation, API compliance, best practices, security) producing a prioritised Critical/Warning/Info report.

Scaffold, lint, review, security-audit, test, and upgrade-verify Helm charts. Runs an interactive interview to build production-ready charts from scratch. Covers chart structure, values design, schema validation, kubeconform, helm diff, and multi-environment scaffolding. Use when asked to "create a helm chart", "lint my chart", "review my helm chart", "check helm security", "generate values schema", "run helm diff", or "add helm tests".

Design, install, debug, review, plan capacity, audit scaling history, migrate from Cluster Autoscaler, and upgrade Karpenter v1.x on EKS. Covers NodePool, EC2NodeClass, NodeClaim, Spot diversity, disruption strategy, Pod Identity/IRSA, interruption queue, private clusters, AMI rotation, and GitOps integration. Use when asked to "set up Karpenter", "debug why nodes aren't provisioning", "review my NodePool", "what would Karpenter provision for this workload", "why did this node terminate", "migrate from CA", or "upgrade Karpenter".

Design, debug, and review KEDA ScaledObject/ScaledJob autoscaling. Covers all major scalers (Prometheus, SQS, Kafka, Redis, Cron, HTTP Add-on, Azure Service Bus), TriggerAuthentication, scaling lifecycle tuning, GitOps integration, and troubleshooting. Use when asked to "add KEDA autoscaling", "debug why my ScaledObject isn't scaling", "review my KEDA config", or "generate a ScaledObject for <trigger>".

Find, live-validate, map the blast radius of, and revoke leaked secrets with Kingfisher (MongoDB) — across a local repo, Git history, a GitHub/GitLab/Bitbucket org, S3/GCS, Docker images, Slack, Jira, Confluence, Teams, or Postman. Covers local CLI scanning, direct validate/revoke without a scan, baseline management (track only new secrets), kingfisher.yaml policy, CI diff-scan gates, and pre-commit/Husky hooks. Use when asked to "scan for secrets", "is this key still live", "what can this credential reach", "revoke this token", "did we leak a secret", or "block new secrets in CI". Pattern-only secret scan bundled with a CVE pass → /platform-skills:trivy. Secrets-context safety in workflow YAML → /platform-skills:zizmor. Storing/rotating secrets inside the cluster → /platform-skills:secrets.

Cluster baseline scaffolding, RBAC diagnosis and generation, workload hardening, and structured pod/scheduling debug for plain Kubernetes across all distributions.

Generate, test, audit, debug, and migrate Kyverno policies using the new CEL-based policy types (ValidatingPolicy, MutatingPolicy, GeneratingPolicy, ImageValidatingPolicy — all apiVersion policies.kyverno.io/v1). Covers matchConstraints, matchConditions, CEL validations/mutations, generator.Apply(), Audit→Deny promotion, PolicyException, kyverno-cli testing, and migration from legacy ClusterPolicy or PodSecurityPolicy. Use when asked to "write a Kyverno policy", "test a ValidatingPolicy", "audit my cluster for violations", "why is my policy not firing", or "migrate from ClusterPolicy".

Linkerd-specific diagnostics — mTLS verification, proxy injection issues, authorization policy debugging, traffic management, and multi-cluster connectivity problems.

Linux administration and networking diagnostics — DNS, load balancing, VPCs, kernel tuning, and connectivity troubleshooting.

MCP server and client development — scaffold, implement tools/resources/prompts, validate schemas, debug protocol compliance, and deploy with auth and rate limiting.

Claude Code skills for Chinese-narration recaps from supported video files, with optional editable JianYing/CapCut draft export. | 用 Claude Code skills 为支持的视频文件…

Drive the Unity Editor from an AI agent or the terminal. The Editor serves MCP itself over HTTP, so there is no second process to run, and the isuzu-unity-cli c…

面向企业的数字员工构建与运行平台：把专业员工的经验、流程与判断标准，固化为可随时上岗、可配置、可审批、可观测的 AI 数字员工。

A local-first, Pi-powered AI agent workspace for Desktop, WebUI, and CLI

660+ muapi-hosted generative-media models plus community-submitted third-party API tools (SEO, enrichment, social, scraping) — one YAML file per entry, browsabl…

A compounding agent OS for recursive agents. Also an open source alternative to Grok Bot and Meta's Muse.

Independent desktop client for OpenCode 2. Manage projects, sessions, parallel agents, requests, and changes on Linux and macOS.

Production agent skills for Claude Code, Cursor, and any SKILL.md harness — Codex fleets, video pipeline, monorepo review bundles, multi-chain explorer.

See and manage what your coding assistants load — skills, commands, subagents, plugins and MCP servers, with real usage.

An Enterprise-Grade Full-Stack RBAC Permission Management System Built with Go + React

Create AI Agents in a No-Code Visual Builder or TypeScript SDK with full 2-way sync. For shipping AI assistants and multi-agent AI workflows.

基于 DeepSeek Harness（DSH）的稳定桌面端，集成Git、内置浏览器与记忆功能 | DeepSeek Harness desktop GUI with local workspaces, Git, browser and memory.

⚡ Control Apache Airflow with natural language via MCP. Chat with your workflows using Claude, GPT, or any LLM — no REST API calls needed. Supports Airflow 2.x…

Open-source CLI, schemas, resolver, and DSH agent tools for DSH Plugin Hub

Pi Coding Agent 中文学习蓝皮书：从安装与第一个可验收任务开始，逐步掌握 Session、Context、Skill、Extension、Subagent 与长期 Agent 工作流。

Self-hosted framework for orchestrating fleets of specialist AI agents — ensemble reasoning and a full agentic coding pipeline, model-agnostic and local-friendl…

Self-hosted, vendor-neutral control plane for your local coding agents (Claude Code & Codex). Run your agents, on any plane.

A practical AI agents handbook covering agent systems, agentic workflows, LangGraph, MCP/A2A, context engineering, agent memory, evaluation, observability, and…

Vibe Coding 从入门到精通教程｜AI 结对编程工作流｜Prompt、Skill、Workflow、上下文管理、codex实战指南

Static security scanner for LLM agents — prompt injection, MCP config auditing, taint analysis. 51 rules mapped to OWASP Agentic Top 10 (2026). Works with LangC…