Explorar skills

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.

Use when creating episodic scripts, ensuring series continuity, adapting story concepts into visual narratives, or preparing scripts with sufficient beats for storyboarding

Non-compliant fixture: handles user content but no wrapping acknowledgment.

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 calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process

Use to assess Privacy by Design compliance and GDPR/data protection alignment for a feature or system.

Spawn specialized OpenAI Codex CLI subagents for code review, debugging, architecture analysis, security audits, refactoring, documentation, comparative evidence adjudication, and autonomous /goal runs via AGENTS.md persona injection (gpt-5.5, gpt-5.5-pro, gpt-5-mini). Triggers on 'delegate to Codex', 'Codex subagent', 'code review agent', 'security audit', 'refactor with Codex', 'goal run', 'auto

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 pipeline, CUT&Tag, SEACR, Henikoff, targeted chromatin, pA-MNase, process CUT&RUN.

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, generate figure legends, create supplementary tables, draft data availability statements, compile tool citations, or aut

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 ENCODE data. Trigger on: heatmap, visualization, genome browser, track hub, IGV, deeptools, signal plot, peak visualizati

Run eval scenarios to benchmark Mycelium effectiveness. Execute tasks using reflexion loop, validate against success criteria, record metrics.

Write comprehensive tests for code including unit tests, integration tests, and end-to-end tests. Use this to ensure code quality, catch bugs, and validate functionality.

Run GGUF models directly, load LoRA adapters, benchmark inference speed, and serve models via llama-server using llama.cpp. Includes Qwen 3.5 serve scripts (9B dense + F16, 35B MoE) with asymmetric KV cache and thinking mode. Secondary to Ollama; use when needing direct model control or LoRA hot-loading. Triggers on 'llama.cpp', 'GGUF', 'LoRA adapter', 'benchmark inference', 'llama-server'.