LLM Mart Basic

Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of E

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak s

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, o

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

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, classify each one against the written distribution-boundary categories, default to withhold on no clean match, and ask the maintainer only where the taxonomy does not settle 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.

Build AI Agents like playing LEGOs. Everything is a Plugin.

The coding agent that answers to you, your model, your machine, your rules.

CI-native agent CLI tool for deterministic pipeline gating.

Local-first cross-platform desktop workspace for Claude Code / agents: multi-agent, Git worktrees, code diffs, skill marketplace, multi-model, Computer Use, tas…

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

A token-efficient MCP server for safe, line-oriented text file editing with partial reads, hash-based conflict detection, and atomic multi-file operations.

Open-source, evidence-driven MCP server for RTL simulation debugging: correlate VCS/Xcelium logs, VCD/FSDB waveforms, SystemVerilog/UVM source, hierarchy, and c…

runs anywhere. uses anything

One macOS app for Claude Code, Codex, and every agent runtime you use — scheduled runs, global hotkey launcher, per-run git worktrees, one review board.

Soul-driven AI agent with permission-hardened tools, token budgets, and multi-channel access. Runs 24/7 from CLI or Telegram.

Email, SMS & phone-call infrastructure for AI agents — send and receive real email and text messages, and place agent-driven outbound voice calls, all programma…

55 MCP tools to drive the Unity Editor from any MCP-compatible AI agent — scenes, GameObjects, prefabs, assets, tests, and builds. OpenClaw gateway included for…

Google Ads MCP + Meta Ads MCP + GA4 in one server for Claude, ChatGPT, Cursor & n8n — 250+ tools, hosted remote MCP, OAuth login, no API keys. By Ryze AI.

Claude Code & Codex 本地 token 追踪 — 状态栏（Codex 业界首创伪 statusline）、GitHub 风格热力图、多模型成本分析。 | Local token tracker for Claude Code & Codex — status line (industry-first…

Empower the Shell to think. Evolve Operations.

🤖 A full-stack Agent Chat Runtime for pre-production validation, built with act, TypeScript, and LangGraph JS combining streaming, multimodal, HITL, and tools…

Cerul — video memory infrastructure for AI products. SDKs, CLI, MCP, and developer integrations.

Stealth headless browser for AI agents — bypass Cloudflare, bot detection, and anti-scraping. Drop-in Puppeteer/Playwright replacement.

Web research for your agents with smart and safe tooling + knowledge store

FuXi is a fast, self-contained AI coding agent that lives in your terminal — edit code, run commands, and drive tools, with cost-aware routing across LLM provid…