Results for “mutations”

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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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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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.

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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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Checks Next.js Server Actions ('use server') for missing authentication/authorization before mutations, missing input validation, and untrusted client-supplied IDs — treating each action as a public HTTP endpoint.

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Designs and reviews offline-first mobile data on every stack — Flutter, native Android, native iOS, React Native and Kotlin Multiplatform. Covers the local store, the outbox of pending mutations, idempotency keys, retry and backoff, conflict resolution, reconnection, and how to test a flaky network deterministically. Use when an app must work without connectivity, when writes are lost or duplicated after reconnecting, or when local and server data disagree.

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Expert in TanStack Query (React Query) — asynchronous state management. Covers data fetching, stale time configuration, mutations, optimistic updates, and Next.js App Router (SSR) integration.

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Use when managing Apple Ads with asc, including OAuth profiles, ad-account discovery, Platform API v1 campaigns and targeting, reports, assets, recommendations, guarded mutations, raw requests, and Campaign Management API v5 migration.

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Use this skill when implementing form submissions, data mutations, or any 'use server' function in Next.js 16. Trigger words: フォーム送信, mutation, 更新処理, 保存, Server Action, use server, useActionState, revalidatePath, データ更新.

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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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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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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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Follow these patterns when implementing activity emission and audit logging in OptAIC. Use for emitting ActivityEnvelopes on mutations (create, update, delete, execute), designing payloads, and ensuring audit compliance.

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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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Focused Signals scout for PostHog projects running A/B experiments. Watches running experiments for validity threats (sample ratio mismatch, multi-variant contamination, exposure stalls, mid-run flag mutations) and lifecycle drift (zombie experiments running long past their useful life, decided-but-still-running experiments, ended experiments whose flags still serve multiple variants). Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.

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Chains a somatic (tumor-normal) SNV/indel and structural-variant pipeline end to end with GATK Mutect2 (or Strelka2), wiring the somatic-specific machinery - panel-of-normals and gnomAD germline-resource priors, GetPileupSummaries/CalculateContamination, and LearnReadOrientationModel FFPE/oxoG orientation-bias filtering fed into FilterMutectCalls. Use when calling somatic mutations from a tumor-normal pair (or tumor-only with PoN caveats), deciding which artifact filter removes which class of false positive, reasoning about VAF/purity/ploidy and clonal-vs-subclonal detection, adding somatic SV/CNV or TMB/MSI/signatures, or routing variants to AMP/ASCO/CAP tier and oncogenicity interpretation (never germline ACMG).

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Cell-free DNA analysis pipeline from plasma sequencing to tumor monitoring. Preprocesses cfDNA reads, analyzes fragment patterns, estimates tumor fraction from sWGS, and optionally detects mutations from targeted panels. Use when analyzing liquid biopsy samples for cancer detection or monitoring.

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Assigns pathogen lineages (SARS-CoV-2 Pangolin via UShER mode; Nextclade clade + QC; pango-designation alias_key.json resolution) and tracks variant frequencies over time using Nextstrain (Augur + Auspice), wastewater deconvolution (Freyja, COJAC, alcov, lineagespot), lineage fitness modelling (Wenseleers / Bedford-Figgins multinomial logistic), and recombinant detection (3SEQ, RDP4, Bolotie). Covers Pangolin pangolin-data version pinning (mandatory for reproducibility), Nextclade dataset versioning (lineage-defining mutations change with dataset), Freyja barcode forward-only date constraint, ARTIC primer scheme version churn (V3 / V4 / V4.1 / V5.3.2 / Midnight 1200) with documented dropout regions, recombinant X-prefix Pango designation lag, GISAID vs INSDC dual-deposition tensions, and the Karthikeyan 2022 wastewater early-detection signal with explicit reproducibility caveats. Use when assigning Pango lineages and Nextclade clades to viral consensus sequences, building Nextstrain Augur surveillance pipelines, deconvolving wastewater pooled samples into lineage frequencies with Freyja, tracking lineage frequencies and growth advantages over time, pinning pangolin-data / Nextclade dataset versions for reproducibility, handling ARTIC primer dropouts (V4.1 amplicons 64 / 76 / 88-90), or running variant 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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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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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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