開発のスキル

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene constraint (pLI, LOEUF) for ENCODE target genes, needs population-specific frequencies for GWAS variants overlapping cCREs, wants to filter variants by rarity before functional annotation, or is interpreting ENCODE CRISPR/MPRA results in the context of population genetics. Also use when the user mentions gnomAD, allele frequency, pLI, LOEUF, constraint, rare variants, population frequency, ExAC, or variant filtering.

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。

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 resolution-aware anchor matching, cross-lab variation, and Hi-C-specific quality metrics.

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.

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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。

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, clinical significance, pathogenic variant, variant classification, clinical variant, disease variant, VUS, benign, likely pathogenic.

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。

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 for formal retractions, corrections, expressions of concern, and — critically — informal contradictions where subsequent studies failed to reproduce key findings. Integrates with PubMed, bioRxiv, and Consensus to provide a trust assessment. Use this skill for ANY publication evaluation, retraction checking, author reliability assessment, or when a user says "can I trust this paper", "is this study reliable", "has this been refuted", or "check this publication".

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。

Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

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。

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 bulk profiles. Covers platform differences (10X Chromium, Smart-seq2, Drop-seq), quality limitations of single-cell data, multimodal integration (RNA+ATAC), and cross-study reproducibility concerns. Also use for cell type annotation, gene detection limits, dropout artifacts, and single-cell data structure in ENCODE.

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。

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), look up gene phenotype associations, or cross-reference ENCODE targets with Ensembl annotations. Also use when the user mentions Ensembl, VEP, variant effect predictor, liftover, assembly conversion, regulatory build, gene lookup, or cross-references between databases.

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。

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.

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。

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.

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。

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.

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。

Detect drift in .arkhe/roadmap/ context files and regenerate them from the current codebase state. Scaffolds context directory if missing. Use when user runs /roadmap:refresh, mentions "refresh context", "update context", "init roadmap", "stale context", or "scaffold roadmap".

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。

Spring Boot 4 REST API implementation patterns. Use when creating REST controllers, REST endpoints, request validation, exception handlers with ProblemDetail (RFC 9457), API versioning, content negotiation, WebFlux reactive endpoints, HTTP clients with @HttpExchange, JSON serialization with Jackson 3, error handling, or CORS configuration. Covers @RestController patterns, Bean Validation 3.1, global error handling, and declarative HTTP clients.

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。

Creates GitHub Pull Requests with existing PR detection, branch pushing, and intelligent title/body generation. Use when user requests to create pull request, open PR, update PR, push for review, ready for review, send for review, get this reviewed, make a PR, share code, request review, create draft PR, submit for review, run /create-pr command, or mentions "PR", "pull request", "merge request", "code review", "GitHub PR", or "draft".

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。

Multi-agent review resolution with trust-but-verify methodology. Accepts a PR number/URL or a local code-review report file. Extracts review comments, verifies each with parallel agents using confidence scoring (0-100), filters false positives, presents a triage report for approval, then applies fixes and replies. Use when user runs /resolve-review, mentions "resolve PR comments", "address review feedback", "fix PR suggestions", "handle review comments", or "resolve review findings".

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。

Lists local and remote git branches that are candidates for cleanup — merged but not deleted, and inactive branches with no commits in a configurable period (default 3 months). Use when user mentions "stale branches", "old branches", "branch cleanup", "prune branches", "dead branches", "unused branches", "inactive branches", "branch hygiene", or asks to "list branches to delete", "find stale branches", or runs /stale-branches command.

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。

Creates isolated git worktrees in .claude/worktrees/ with intelligent branch naming, auto-incrementing, and commit type detection (feat/fix/refactor). Supports manual descriptions and auto-generation from uncommitted git changes. Use when user requests to create worktree, start isolated work, parallel development, run /worktree command, or mentions "worktree".

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。

Creates context-aware git commits with smart pre-commit checks, submodule support, and conventional commit message generation. Use when user requests to commit changes, stage and commit, check in code, save work, save changes, push my code, finalize changes, add to git, create commits, run /commit command, or mentions "git commit", "commit message", "conventional commits", "stage files", "git add", or needs help with commits.

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。

Deletes merged git branches (local and remote) and flags stale unmerged branches for manual review. Use when user mentions "cleanup branches", "delete merged branches", "prune old branches", "remove stale branches", "branch cleanup", or runs /cleanup-branches command.

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。

Multi-agent code review using the Pragmatic Quality framework. Orchestrates parallel review agents (CLAUDE.md compliance, bug scanning, git history, security) with independent confidence scoring to produce high-signal findings. Use when user runs /code-review, /review:code-review, requests a "code review", "review my changes", "PR review", or mentions "review diff", "review branch".

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。

Explains complex code through clear narratives, visual diagrams, and step-by-step breakdowns. Use when user asks to explain code, understand algorithms, analyze design patterns, wants code walkthroughs, or mentions "explain this code", "how does this work", "code breakdown", or "understand this function".

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。