LLM Mart Basic

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.

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,

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

Validate application configuration with schemas, per-environment rules, runtime checks, and secure handling of sensitive values

Preflight a DGX Spark system for an ML training or inference workload and emit env-report.json

Set up debugging and tracing with remote debugging, distributed tracing, debug logging, profiling, and production diagnostics

Generate API, architecture, code, and user documentation from a codebase and automate keeping it current

Analyze and resolve errors across the full application lifecycle — from stack traces to distributed tracing — using systematic root-cause analysis and observability tools.

Set up error tracking and monitoring — implement structured logging, configure alerts, and integrate with error tracking services for real-time error detection.

Coordinate specialized review agents in parallel or in sequence and synthesize their findings into one code review

Analyze and resolve errors across the full application lifecycle — from stack traces to distributed tracing — using systematic root-cause analysis and observability tools.

Set up error tracking and monitoring — implement structured logging, configure alerts, and integrate with error tracking services for real-time error detection.

AI-assisted smart debugging — parse error messages, stack traces, and failure patterns to identify root causes and produce a fix with automated observability steps.

Generate comprehensive migration plans and scripts for transitioning codebases between frameworks, languages, versions, or platforms with minimal disruption.

Plan and execute safe, incremental dependency upgrades with minimal risk — including breaking-change migration paths and proper test verification.

Orchestrate legacy system modernization using the strangler fig pattern with gradual component replacement

Scaffold React and React Native components with TypeScript, tests, styles, and Storybook stories

Scan React, Vue, Angular, and vanilla JavaScript code for XSS vulnerabilities and report fixes with secure coding examples

Orchestrate end-to-end full-stack feature development across backend, frontend, database, and infrastructure layers

Orchestrate git workflow from code review through PR creation with quality gates

Create a role-specific onboarding plan for a new team member, from pre-arrival setup through the first 90 days

Enhance a pull request with a generated description, review checklist, risk assessment, and test coverage report

Orchestrate multi-agent incident response with modern SRE practices for rapid resolution and learning

Make any song you can imagine

Leading AI-powered video generation platform that specializes in creating hyper-realistic talking avatars

Hermes Agent is an open-source, self-improving autonomous AI agent developed by Nous Research

Kilo Code is a popular, open-source AI coding agent and "agentic engineering" platform designed to help developers build, refactor, and debug software faster

General-purpose agent in one static Go binary. ReAct loop, ACP server for IDEs, OpenAI-compatible REST API with embedded web UI, Telegram gateway, cron schedule…

Autonomous agent framework with structured memory, safety hooks, and loop management. Built by the agent that runs on it.

TSP自托管、零运维的 A 股「选股 + 监控 + 回测」量化工作台 | 基于 TickFlow 数据源 | LLM能力驱使策略定制+个股分析+复盘 | 自由接入第三方数据源与个性化扩展数据 | 个人开源 ,非TickFlow官方项目

Curated, verified Agent Skills powered by ModelStudio.

Run Claude Code, Codex, Antigravity, Cursor Agent and OpenCode as one runtime — persistent sessions, multi-agent councils, an OpenAI-compatible endpoint, an MCP…

pi had nothing (nothing), so I made something (something) — sorry mariozechner-senpai, I went ahead and lovingly soiled your pure pi for you. opinionated fork o…

A persistent workspace for development work that self-improves and continues beyond one session.

Open-source memory and context for user-aware agents: scoped memory, provenance, retrieval quality, correction, boundaries, evals, and MCP/HTTP access.

📚 A zero-dependency, git-backed micro-lesson library for AI Agents to asynchronously share and search verified debugging experience. Python stdlib only. | http…

Deterministic, local-first memory and guardrails for AI coding agents with no LLM in the hot path.

Deterministic spec-orchestration for local LLMs in the pi coding agent — drives prompts through refine→research→grill→compose→critique, with bundled web/docs/fe…

Native Safari browser automation for AI agents. 97 tools via AppleScript — zero overhead, keeps logins, runs silently in background. Drop-in alternative to Chro…

Agent OS: keep specialist agents in a hub, spin up a temporary orchestrator per task. Local-first, works with any model.

Git for agent memory. Branches, diffs, PRs, and rollback for what your agents know.

Multi-Provider AI Gateway - No personal logs by design. Model autodiscovery, Failover groups, High availability, Android companion app, and more - "Because we h…

Production-grade MCP server for MikroTik RouterOS with secure AI-native network automation.