4,279 件 ・ 関連度順
概要と使いどころ
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 files. Trigger on: WGBS pipeline, bisulfite sequencing, methylation calling, DNA methylation pipeline, bismark, bwa-meth, bedMethyl.
日本語の概要は準備中です。原文の説明を表示しています。
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, or generate summary reports. Trigger on: batch analysis, multiple experiments, bulk processing, experiment comparison, batch QC, multi-sample, batch download, experiment table, summary report, collection analysis.
日本語の概要は準備中です。原文の説明を表示しています。
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 novo motif, motif enrichment, findMotifsGenome, AME, MEME-ChIP, known motif, TF binding motif, co-factor, motif discovery.
日本語の概要は準備中です。原文の説明を表示しています。
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 conformation, contact matrix, loop calling, TAD detection, Juicer, HiCCUPS, 3D genome.
日本語の概要は準備中です。原文の説明を表示しています。
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 nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.
日本語の概要は準備中です。原文の説明を表示しています。
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, genome-wide association, SNP association, trait association, GWAS Catalog, disease association, risk variant, lead SNP, LD proxy.
日本語の概要は準備中です。原文の説明を表示しています。
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 database, binding profile, PWM, position weight matrix, TF motif, motif enrichment, motif scanning, binding site prediction.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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 correlation, chromatin state segmentation, enhancer-gene linkage, or any analysis that requires merging or comparing data from two or more ENCODE experiments. Covers same-assay cross-sample, multi-omic same-sample, cross-organism, and perturbation integration designs. Guides compatibility checks, batch effect detection, normalization, integration strategy selection, and provenance documentation.
日本語の概要は準備中です。原文の説明を表示しています。
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 on: CellxGene, single-cell atlas, cell type expression, Census, cell type specificity, single-cell context, scRNA-seq atlas.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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.
日本語の概要は準備中です。原文の説明を表示しています。
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 ChIP-seq, MACS2 peak calling, IDR analysis, ChIP-seq FASTQ processing.
日本語の概要は準備中です。原文の説明を表示しています。
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 expression levels, expression atlas, eQTL, tissue-specific expression, TPM values.
日本語の概要は準備中です。原文の説明を表示しています。
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 distance, nearest gene.
日本語の概要は準備中です。原文の説明を表示しています。
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 matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.
日本語の概要は準備中です。原文の説明を表示しています。
Guide users through structured collaborative documentation creation. Use when user wants to write documentation, update README, create architecture docs, draft proposals, technical specs, decision docs, refactor documentation, create API docs, or document code.
日本語の概要は準備中です。原文の説明を表示しています。
Orchestrates 6-phase SDLC pipeline (discovery, requirements, architecture, workstreams, implementation, summary) for guided feature development. Use when user runs /core:develop command, requests spec-driven development, wants to create implementation plans with architecture decisions, or mentions "SDLC", "spec-driven", "plan feature", "development pipeline". Supports plan persistence, wave-based resume, autonomous mode, and architecture/implementation verification.
日本語の概要は準備中です。原文の説明を表示しています。
Audit, classify, validate, and scaffold documentation using the Diataxis framework (Tutorials, How-to guides, Reference, Explanation). Use when user mentions "diataxis", "documentation framework", "quadrant", "doc audit", "doc coverage", "collapsed document", "tutorial vs how-to", "quadrant purity", "documentation types", or wants to classify docs by type.
日本語の概要は準備中です。原文の説明を表示しています。
Interactive Claude Code environment setup wizard. Detects existing configuration, guides through best-practice setup for Global CLAUDE.md, project scaffolding, MCP servers, hooks, custom agents, keybindings, and settings. Use when user runs /devtools:code-env-setup, mentions "setup claude code", "configure claude", "claude code setup", "environment setup", or "initialize claude code".
日本語の概要は準備中です。原文の説明を表示しています。
Audit a site or page against Google's OFFICIAL AI optimization guidance — readiness for AI Overviews and AI Mode, grounded in Google's published ai-optimization-guide and ai-features docs (not third-party GEO theory). Use when user says "AI optimization", "AI Overviews", "AI mode", "AI search readiness", "optimize for AI", or "GEO audit".
日本語の概要は準備中です。原文の説明を表示しています。
Diátaxis Documentation Expert. An expert technical writer specializing in creating high-quality software documentation, guided by the principles and structure of the Diátaxis technical documentation authoring framework.
日本語の概要は準備中です。原文の説明を表示しています。
Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This workflow helps users efficiently transfer context, refine content through iteration, and verify the doc works for readers. Trigger when user mentions writing docs, creating proposals, drafting specs, or similar documentation tasks.
日本語の概要は準備中です。原文の説明を表示しています。
Guideline for designing, implementing, and verifying secure TypeScript and JavaScript applications following OWASP Top 10 best practices. Use when the user wants to: (1) review TypeScript or JavaScript code for security vulnerabilities, (2) design a secure Node.js, Deno, or browser application architecture, (3) implement security features (authentication, authorization, cryptography, input validation), (4) audit npm/yarn/pnpm dependencies for known vulnerabilities, (5) create security checklists or verification plans, (6) fix security bugs or harden existing TypeScript or JavaScript code, (7) set up security testing and static analysis (ESLint security plugins, Semgrep, Snyk), or (8) handle any TypeScript/JavaScript security concern including injection prevention, prototype pollution, XSS protection, SSRF prevention, secrets management, and secure deployment.
日本語の概要は準備中です。原文の説明を表示しています。