LLM Mart Basic

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

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

Add remote HTTP or local stdio MCP servers to Claude Code, choose the right scope, protect credentials, verify the connection, and test with least privilege.

Skills teach Claude a repeatable method, connectors provide governed access to apps and live data, and plugins package related capabilities for installation and sharing.

Use an agent skill to package reusable know-how and workflow instructions. Use an MCP server when an agent needs live, governed access to external data or actions.

Custom commands and skills can both create a slash-invoked workflow in Claude Code. The important choice is how the workflow is discovered, shared, and permissioned.

A useful Claude skill solves one recurring engineering job, is easy to inspect, and saves more time than it creates in setup and review.

Claude skills can live in your Claude account, your local Claude Code setup, or a repository. Install them where the sessions that need them can load them.

Build a portable AI agent skill from one repeatable job: a precise description, concise instructions, focused resources, and tests that prove it works.

AI agent skills package instructions, scripts, references, and templates into portable folders an agent loads only when the task calls for them.

AI made publishing cheap, which is exactly the problem. What separates a page worth ranking from a competent summary of the first ten results.

A prompt that works once isn't a quality system. Five cases, an observable rubric, and a regression set will tell you whether a change helped.

One character of YAML, four pods that never started, and two safety nets I didn't know were holding. Every restart is an audit. Schedule them before they schedule you.

"Verify your work" isn't an instruction. It's a mood. Here's the version that's an instruction. Verify with a different mechanism than the one that made the claim.

A prompt that works once may still fail in production. A lightweight eval set gives you repeatable cases, a clear rubric, and a way to see whether a prompt change actually improved the workflow.

The best AI tool is not the one with the longest feature list. It is the one that solves a defined job reliably, fits the workflow, handles data appropriately, and remains useful after the novelty wears off.

Use AI to speed research without losing trust. Learn to find primary sources, verify claims, preserve uncertainty, and keep an auditable source trail.

Better prompts aren't magic wording. They're short briefs that hand the model a task, the context it can't infer, the limits, and a quality bar.

A green PR, a controller reporting success, and not one line of the new code running

Discover testnet↔mainnet subnet lineage from repo configs and open a PR for review (pass --dry-run to report only)

Triage raw inbox notes into reviewed repository destinations without deleting their sources.

Audit and rewrite content to remove AI writing patterns

Log a completed piece of content to content/log.md after the user confirms it was published.

Validate a dream artifact, review each proposal, and apply only individually accepted changes.

Run a curator pass against the validated memory directory and produce a proposal artifact.

End a session — log what happened, update state and the decision log, propose memory updates, and check for uncommitted or unpushed work

Find relevant context files by topic. Use when you need to load files for a topic without a slash command, or when a task spans multiple domains.

Inventory and migrate selected Gemini CLI workflows with dry-run review and parity checks.

Find repeated workflows in selected Gemini CLI sessions and draft portable skills after review.

Scan multi-session drift and offer individually reviewed fixes only after explicit approval.

Scan orphaned worktrees and stale branches, then offer explicit approval-gated cleanup.

Guided onboarding or import for durable workspace context

Start a session — load state files, flag staleness, and give a briefing on current priorities, deadlines, and blockers

Create a morning heartbeat from repository state and update the local heartbeat log.

Mid-session checkpoint — append progress to today's session log and update state files if a priority shifted, without ending the session

Maintainer-only. Find every file that would newly ship to adopters and decide, one file at a time, whether to ship it or withhold it. Drives the release CLI, which refuses to produce a manifest until every shipping file has an answer.

Audit memory, wiki, and auto-loaded files for duplication, conflicting instructions, and stale content. The default path researches, then asks you a single Apply / Discuss / Decline question; on Apply it applies the report, files any out-of-scope problem as a tech-debt issue, then commits, opens a PR, and merges it on a main-branch run like /update-deps. Pass --apply to re-run the apply-and-publish stage against the most recent report.

Fix the tech-debt backlog, a single issue or a recommended related batch, highest severity then oldest first, on a fresh isolated branch through the audit gate, closing the issue(s) on merge. Pass `list` to see the ordered backlog, `why <issue-number>` to explain the recommendation, or a bare `<issue-number>` to fix that issue directly.

Health-check and auto-heal this project's Claude integration, triage, heal, verify, and report an F-to-A+ grade.

Paper trading simulator for Polymarket — built for AI agents. MCP server, live order books, strategy backtesting. Install: npx clawhub install polymarket-paper-…

An SSH tool dedicated to addressing all pain points · (macOS/Windows/Linux/Android/iOS)

The first AI agent harness native to the browser. A browser extension that runs a full agent loop where you already work: it drives your tabs, spins up sandboxe…

SmartLabel AI 2026: Auto-Annotate Any Object via LLM-Powered Prompt Parsing

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

Scholar All-In-One: A research infrastructure for AI agents

Give your AI agent a real browser — with a human in the loop. Open-source MCP-native browser agent.

同花顺免费开源AI插件FQGate-agent（原插件名 tonghuasun-agent）：为 Codex、Claude Code、DeepSeek 等 AI 工具提供本机 A 股实时行情、K 线、Level-2、资讯、账户查询与可选交易能力。

A non-linear AI agent workbench — session is a tree: branch anytime, and context follows the branch

Production-grade AutoCAD MCP server for AI agents — 122 tools, dual COM (live AutoCAD) + headless ezdxf engines, ISO GD&T and dimension-tolerance validation for…

A DeepSeek coding agent harness: persistent shell, Ultra subagents, auto approval, Chrome MCP and session telemetry

Waku Waku! Waku Agent is a local-first AI agent harness you actually own, including loop, memory, eval, all in code built to stay legible as it grows.

Remote control for Claude Code, Codex, Grok, and Cursor on Mac or PC. View sessions, send tasks, and drive them remotely from your phone, PIN, or Ring. OpenClaw…

Next-gen AI-native server ops panel with an in-workspace SRE agent. Crash self-healing, safe rollbacks, Docker/game servers, and local Ollama support.

Professional cloud architecture diagrams with official AWS, Azure and GCP icons, from Terraform code or a plain JSON graph. MCP server + agent skill.

A ready-to-use self-growing desktop AI assistant for long-running tasks, memory, agents, tool reviews, MCP, and high-concurrency workspace automation. / 开箱即用的自我…

Collection of templates using the Alchemyst AI Platform for your next big AI app.

Fast, exact LLM decoding on Apple Silicon (MLX) behind an OpenAI-compatible endpoint

The open source AI research agent.