LLM Mart Basic

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.

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs

Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a collection of experiments, manage citations, compare experiments, or track data provenance.

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under

Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact o

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.

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.

Your Personal AI Assistant; easy to install, deploy on your own machine or on the cloud; supports multiple chat apps with easily extensible capabilities.

Agent OS: the agent gets smarter on its own. We just hold the line: the grading command and expected result never make it into the success contract we hand it.…

Curated systems, benchmarks, and papers etc. on memory for LLMs/MLLMs --- long-term context, retrieval, and reasoning.

:memo: Vimlike Modal Text Editor in Rust

CI-native security testing for MCP servers. Attack simulation, schema drift detection, and health scoring before agents depend on them.

Hermes Agent memory plugin/provider for scope-aware recall, SQLite truth, LanceDB semantic search, and hybrid retrieval.

For You Agent——AI 时代的个人随身数字人格。把你的模型、AI 账号、技能、提示词和工作方式，带到每一个 AI 工具里。

A coding agent: give it a prompt and it reads, writes, runs commands, and searches code in a loop until the work is done, using native tool-calling across OpenA…

A secure persistent personal agent server in Rust. One binary, sandboxed execution, multi-provider LLMs, voice, memory, Telegram, WhatsApp, Discord, Teams, and…

Self-evolving agent: grows skill tree from 3.3K-line seed, achieving full system control with 6x less token consumption

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

See your agent think. Zero-config observability & governance for 26 AI agent runtimes: Claude Code, Cursor, OpenAI Codex, GitHub Copilot, Gemini CLI, Cline, Ope…

Save 94% on AI coding tokens. Index your codebase, agents search instead of reading files. Works with Claude Code, Codex, Copilot, Cursor, Gemini CLI. Local MCP…

Yet another coding agent harness, lightweight and written in go.

a coding Agent from pi. ∞ providers, sub-agents, hashline edits, and a permission gate

Omnigent is an open-source AI agent framework and meta-harness: orchestrate Claude Code, Codex, Cursor, Pi, and custom agents — swap harnesses without rewriting…

🧠 Leon is your open-source personal assistant.

The Station, an open-world multi-agent environment that models a miniature scientific ecosystem.

The Frontend Stack for Agents & Generative UI. React, Angular, Mobile, Slack, and more. Makers of the AG-UI Protocol

VelaTerm = iTerm2 + Codex, The Best Terminal for AI Coding