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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, calling loops or TADs. Trigger on: Hi-C pipeline, chromatin conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome.

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.

Heuristic-candidate fixture: outside curated list but strong user-content signal.

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: DNase-seq pipeline, DNase hypersensitive, DHS, Hotspot2, footprinting, DNase I, chromatin accessibility DNase.

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 annotation, ChIPseeker, GREAT, peak to gene, genomic feature, promoter enrichment, gene ontology, peak distribution, TSS

Use when facing a new problem to classify its domain (Clear, Complicated, Complex, Chaotic, Confused) and select appropriate methods.

One command from "plugin installed" to "running brief on your idea." Combines /mycelium:setup (project-state initialization) and /mycelium:interview (10-minute discovery brief) into a single flow. Run this immediately after installing the Mycelium plugin — it's the recommended entry point for first-time users.

Use when starting implementation on a new or unfamiliar codebase. Auto-detects tech stack and sets up development context.

Use before any research activity or significant decision. Reviews cognitive biases relevant to the current stage.

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 overlap for ENCODE regions, convert coordinates between GRCh37 and GRCh38, resolve gene IDs (Ensembl ↔ symbol ↔ RefSeq), loo

A comprehensive design operating system synthesized from 10 canonical design books. Covers research, typography, color theory, composition, branding, logo design, storytelling, web design, creative process, and professional practice.

Sandbox de civilização de IA onde você, como um agente digital, vive e se desenvolve da sobrevivência à prosperidade. Inclui registro de agente, criação de personagem, sistema de crédito e interações sociais.