「mutations」の検索結果

Assigns pathogen lineages (SARS-CoV-2 Pangolin UShER mode; Nextclade clade + QC; pango-designation alias resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage-fitness modelling (multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data and Nextclade dataset version pinning (mandatory; lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme churn (V3/V4/V4.1/V5.3.2/Midnight) with dropout regions, and recombinant X-prefix designation lag. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater into lineage frequencies with Freyja, tracking lineage frequencies over time, handling ARTIC primer dropouts, or running surveillance for SARS-CoV-2/influenza/Mpox/RSV/H5N1/measles.

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Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.

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Detect single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Audit whether tests detect broken behavior by tracing assertions and running narrow controlled mutations in an isolated workspace; use for test-quality reviews, not routine test execution.

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Decides HOW to mutate a DAG when a node fails, quality is below threshold, or new information changes the plan. Selects from mutation strategies (add node, replace agent, fork paths, loop back, downgrade model) based on failure type, cost budget, and execution history. Activate on "DAG failed how to fix", "mutation strategy", "replan on failure", "adaptive DAG", "recovery strategy", "what to do when node fails". NOT for detecting failures (use dag-quality), executing mutations (use dag-planner), or runtime execution (use dag-runtime).

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Determines when to test for germline KCNJ5 mutations indicating familial hyperaldosteronism type III in very young patients with primary aldosteronism. Triggered by severe early-onset hypertension with hypokalemia in infants or young children (<20 years) with confirmed PA.

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Expert-level discrete mathematics knowledge. Use when working with logic, set theory, combinatorics, graph theory, relations, functions, induction, recursion, boolean algebra, or discrete probability. Also use when the user mentions 'combinatorics', 'permutations', 'combinations', 'pigeonhole principle', 'inclusion-exclusion', 'generating functions', 'recurrence relations', 'graph theory', 'trees', 'logic', 'propositional calculus', or 'boolean algebra'.

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Build, extend, validate, and publish a ChatGPT Sites application whose durable database and backend functions run on Convex. Use when a user invokes $codex-sites-convex, selects this skill from the skill picker, asks for a ChatGPT Site backed by Convex, or asks to add Convex data, realtime queries, mutations, authentication, files, schedules, or actions to an existing ChatGPT Sites project.

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Guide for when to use and when not to use return validators in Convex functions. Use this skill whenever the user is writing Convex queries, mutations, or actions and needs guidance on return value validation. Also trigger when the user asks about Convex type safety, runtime validation, AI-generated Convex code, Convex AI rules, Convex security best practices, or when they're debugging return type issues in Convex functions. Trigger this skill when users mention "validators", "returns", "return type", or "exact types" in the context of Convex development. Also trigger when writing or reviewing Convex AI rules or prompts that instruct LLMs how to write Convex code.

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Create Convex queries, mutations, and actions with proper validation, authentication, and error handling. Use when implementing new API endpoints.

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Convex backend specialist. Use this agent for any code inside a `convex/` directory — function definitions, schemas, indexes, queries, mutations, actions, HTTP endpoints, cron jobs, file storage, auth wiring, and component installation. Knows the object-form function syntax, validator patterns, resource limits, and component ecosystem that generic Claude routinely gets wrong.

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Full-stack Convex development guidelines covering React, Vite, TypeScript, mutations, auth, design system, and documentation practices. Use when building features, writing Convex functions, or making code changes in this project.

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Design and build reactive, type-safe, production-grade backends on Convex. Covers schema, queries/mutations/actions, indexes, auth, file storage, scheduling, real-time multiplayer, mobile backends, and LLM/agent workflows on Convex's one-platform stack.

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 when to use and when not to use return validators in Convex functions. Use this skill whenever the user is writing Convex queries, mutations, or actions and needs guidance on return value validation. Also trigger when the user asks about Convex type safety, runtime validation, AI-generated Convex code, Convex AI rules, Convex security best practices, or when they're debugging return type issues in Convex functions. Trigger this skill when users mention "validators", "returns", "return type", or "exact types" in the context of Convex development. Also trigger when writing or reviewing Convex AI rules or prompts that instruct LLMs how to write Convex 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。

Create Convex queries, mutations, and actions with proper validation, authentication, and error handling. Use when implementing new API endpoints.

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。

Design and build reactive, type-safe, production-grade backends on Convex. Covers schema, queries/mutations/actions, indexes, auth, file storage, scheduling, real-time multiplayer, mobile backends, and LLM/agent workflows on Convex's one-platform stack.

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。

Convex backend specialist. Use this agent for any code inside a `convex/` directory — function definitions, schemas, indexes, queries, mutations, actions, HTTP endpoints, cron jobs, file storage, auth wiring, and component installation. Knows the object-form function syntax, validator patterns, resource limits, and component ecosystem that generic Claude routinely gets wrong.

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。

Full-stack Convex development guidelines covering React, Vite, TypeScript, mutations, auth, design system, and documentation practices. Use when building features, writing Convex functions, or making code changes in this project.

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 typosquatting, homograph phishing, and brand impersonation domains using dnstwist to generate domain permutations and identify registered lookalike domains targeting your organization.

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Uses the gh-axi CLI for GitHub shell operations: issue, pull request, workflow run, release, repo, search, and API tasks. Prefer this over regular `gh` for GitHub reads and simple mutations when an agent needs compact, structured, suggestion-rich output. Triggers on: gh, GitHub CLI, github issue, github pr, pull request, workflow run, github release, gh api, repo inspection, list PRs, view issue, check workflow runs, inspect repo, GitHub shell operations.

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Manage Railway projects, services, deployments, environments, variables, and deployment logs via Railway's public GraphQL API — one endpoint, relay-style pagination, two token flavors (account vs project), typed mutations for deploys and env vars. Use when the user wants to deploy, check service status, manage env vars, or read deployment logs programmatically without the Railway MCP installed.

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Troubleshoot and inspect a BGW320 home network through this repo's TypeScript/Bun gateway CLI. Use when working on read-only router status checks, device inventory, broadband/fiber/firewall/Wi-Fi diagnostics, JSON capture, sweep/audit coverage, fixture capture, dry-run router mutations, guarded commits, and safe handling of secrets or device information.

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。