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Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based prioritizers, integrating multi-evidence streams (fine-mapping, colocalization, ABC enhancer-gene, distance, chromatin), reconciling discordant L2G vs PoPS calls, prioritizing tissue-specific eQTL evidence, or triangulating across at least three independent lines of evidence for a publication-grade effector-gene nomination.

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Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.

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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR), colocalization, fine-mapping with SuSiE / FOCUS, mediation, TWAS triangulation, cis-pQTL drug-target MR, effector-gene prioritization (L2G / PoPS / cS2G), and GenomicSEM common-factor GWAS. Use when triangulating causal inference across multiple complementary methods, prioritizing tissues via stratified LDSC, nominating or de-risking drug targets, mapping a lead SNP to a candidate effector gene, modeling shared genetic architecture across correlated traits, or producing a STROBE-MR-compliant publication-grade evidence battery from GWAS summary statistics.

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Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.

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Internal — for Boundless team members only. Query the Boundless Indexer REST API for on-chain market data, staking, PoVW rewards, delegations, and market efficiency on prod/staging environments. Use when the user asks about proof requests, provers, requestors, staking data, PoVW rewards, delegations, market aggregates, leaderboards, or wants to fetch data from the indexer API on live networks. Also use when the user mentions "indexer" and wants to look up addresses, requests, or market statistics on deployed environments. Do NOT use for debugging local code changes, reviewing PRs, or investigating issues in the codebase itself.

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Internal — for Boundless team members only. Query AWS CloudWatch logs for Boundless services (provers, slasher, distributor, order stream, order generator, indexer, signal) on prod/staging environments. Use when the user asks to look at service logs, debug service behavior from log output, search logs for a request ID, or investigate errors using CloudWatch. Do NOT use for debugging local code changes, reviewing PRs, or investigating issues in the codebase itself.

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。

Internal — for Boundless team members only. Query Boundless broker telemetry tables on Redshift for prod/staging operational data. Use when the user asks about broker health, request evaluations, request completions, proving times, skip rates, telemetry data, or wants to run SQL against the telemetry database on live networks. Also covers historical telemetry through 2026-04-24 stored as Parquet archives in S3 (queried via DuckDB). Do NOT use for debugging local code changes, reviewing PRs, or investigating issues in the codebase itself.

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Internal — for Boundless team members only. Help developers deploy Boundless AWS infrastructure to the dev environment. Use when the user wants to deploy a service to dev, bootstrap their dev environment, troubleshoot infrastructure issues, or understand what env vars a service needs. Also handles teardown and status checks.

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Start and interact with the Boundless localnet (docker compose-based local development network). Covers dev mode (fake proofs, broker included) and full proving mode, submitting requests, and debugging order flow. Use when the user wants to start localnet, run the local network, test proof requests locally, or debug broker/order-stream issues.

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Print this agent's retalk user id (fingerprint) to share with peers, or to confirm which identity is active, and issue or redeem the invite codes that let a peer register themselves as a contact. Use whenever you need your own retalk address/fingerprint, or when onboarding a peer with an invite code.

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Use this skill when asked to perform any of the following actions in a Java project: - To add jspecify support - To prevent NullPointerExceptions - To better handle Nullability This skill will add jspecify dependency, configure Maven or Gradle build to automatically use jspecify for checking Nullability issues.

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Optimize MATLAB code for better performance through vectorization, memory management, and profiling. Use when user requests optimization, mentions slow code, performance issues, speed improvements, or asks to make code faster or more efficient.

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Use when tutoring a learner through MATLAB debugging, error interpretation, failed tests, incorrect outputs, array-shape problems, indexing mistakes, function argument issues, or code repair practice. Use for guided debugging sessions, debugging drills, teach-the-agent critique, and evidence-based MATLAB troubleshooting.

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Configure this repo for the engineering skills: set up its issue tracker, triage label vocabulary, and domain doc layout. Run once before first use of the other engineering skills.

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Plan a huge chunk of work (more than one agent session can hold) as a shared map of decision tickets on your issue tracker, and resolve them one at a time until the way to the destination is clear.

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Review the changes since a fixed point (commit, branch, tag, or merge-base) along two axes: Standards (does the code follow this repo's documented coding standards?) and Spec (does the code match what the originating issue/spec asked for?). Runs both reviews in parallel sub-agents and reports them side by side. Use when the user wants to review a branch, a PR, work-in-progress changes, or asks to "review since X".

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。

Move issues and external PRs through a state machine of triage roles, categorise, verify, grill if needed, and write agent-ready briefs.

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。

Turn the current conversation into a spec and publish it to the project issue tracker: no interview, just synthesis of what you've already discussed.

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。

Validate database integrity, test migrations forward and backward, verify schema constraints, manage seed data, detect migration drift, and identify query performance issues. Covers PostgreSQL, MySQL, MongoDB with Prisma, TypeORM, Drizzle, and SQLAlchemy, plus Testcontainers test databases. Use when: "database test," "migration test," "migration rollback," "rollback test," "data integrity," "SQL test," "schema validation," "seed data," "query performance," "Testcontainers." Not for: synthetic data generation/masking at scale — use test-data-management; Docker/IaC test-environment provisioning — use test-environments; SQL injection — use security-testing. Related: test-data-management, test-environments, security-testing, ci-cd-integration.

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。

Test for WCAG 2.2 AA compliance with axe-core + Playwright, keyboard navigation audits, screen reader testing, ARIA pattern validation, and legal compliance mapping (ADA, EAA, Section 508). Automated tools catch 30-40% of issues — this skill covers automated and manual testing together. Use when: "accessibility," "a11y," "WCAG," "screen reader," "axe," "keyboard navigation," "ARIA," "ADA compliance." Not for: cookie-consent/GDPR compliance — use compliance-testing; pixel-diff visual regression — use visual-testing. Related: playwright-automation, compliance-testing, visual-testing, ci-cd-integration.

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Review EXISTING test code for quality, smells, and testability issues. Detects test smells across six dimensions — readability, reliability, diagnostic value, design, AI-generated, and coverage — analyzes testability of application code, and backs the qualitative smells with mutation testing. Use when: "review my tests," "test quality audit," "test smells," "testability analysis," "are these tests any good." Not for: generating new tests — use `ai-test-generation`. Not for: testing AI features in your product — use `ai-system-testing`. Related: unit-testing, shift-left-testing, coverage-analysis, ai-test-generation.

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。

Review PR comments from GitHub. Fetches inline review comments and issue comments, classifies by blocking vs non-blocking, and summarizes actionable items.

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Review the working-tree changes (vs main) for correctness, concurrency, architecture, testing, and API/doc issues — following .github/CODE_REVIEW.md — and return a severity-graded report. Scales the machinery to the diff size: a single code-reviewer agent for a small change, or a fan-out-and-verify Workflow for a large/multi-unit one. Produces findings; it does not apply fixes (the caller does).

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。