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Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

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Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

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Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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Azure AI Document Translation SDK for batch translation of documents with format preservation. Use for translating Word, PDF, Excel, PowerPoint, and other document formats at scale.

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Azure Batch SDK for Java. Run large-scale parallel and HPC batch jobs with pools, jobs, tasks, and compute nodes.

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When the user needs to generate, iterate, or scale ad creative for paid advertising. Use when they say 'write ad copy,' 'generate headlines,' 'create ad variations,' 'bulk creative,' 'iterate on ads,' 'ad copy validation,' 'RSA headlines,' 'Meta ad copy,' 'LinkedIn ad,' or 'creative testing.' This is pure creative production — distinct from paid-ads (campaign strategy). Use ad-creative when you need the copy, not the campaign plan.

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Act as a senior Amazon account growth operator that combines Amazon performance-drop analytics, Amazon growth-opportunity analytics, Amazon Ads data, retail readiness, BSR/rank signals, margin, inventory, and campaign/search-term evidence into a prioritized profitable growth action plan. Use when Codex needs to decide what to protect, fix, scale, reduce, pause, harvest, launch, or monitor for an Amazon brand, agency, marketplace, ASIN set, or account; when building daily, weekly, or monthly Amazon account operating plans; when reallocating ad budget; when deciding which ASINs are safe or risky to push; or when turning performance-drop and growth-opportunity findings into approval-gated actions with success/failure criteria.

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Measure, root-cause, fix, verify and record performance contention on a developer machine: cloud-sync daemons (iCloud Drive, OneDrive, Dropbox, Google Drive), file indexers, AI-tool MCP server fleets, and automation browsers left behind by tests and browser skills. Trigger when the machine is slow, apps freeze, browser or MCP tool calls time out, load exceeds the core count, or before and after any UI/UX/performance test run. Includes the L0–L4 optimisation scale and the test-hygiene contract.

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Turns a vague "what should we do about X" into a scored decision - explicit actions, an explicit unknown, an explicit prior, and one utility scale - then picks by maximum expected utility and checks the result for framing effects. Use when facing a choice between options under uncertainty, when a decision has stalled in circular debate, when someone asks "should we do A or B", or before writing any decision record, strategy memo, or roadmap commitment.

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Expert-level nanomaterials engineering covering synthesis, characterization, properties at nanoscale, nanocomposites, safety, and industrial applications of nanomaterials.

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Expert-level reaction engineering covering reaction kinetics, reactor design, ideal and non-ideal reactors, catalysis, and reactor scale-up.

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Expert-level meteorology covering atmospheric dynamics, thermodynamics, synoptic meteorology, mesoscale systems, numerical weather prediction, and climate dynamics.

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Drive QA of a SwiftUI app on a real iPhone over USB - screenshot, read the accessibility tree, inspect @Observable state, tap, swipe, and type through an HTTP bridge embedded in the app under test. Use when asked to test an iOS app on a physical device, find bugs on the device, or expose a connected iPhone to a remote agent over Tailscale. Requires the ios-agent-qa runtime; not for simulator or XCTest work.

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When the user wants to audit, review, or diagnose SEO issues on their site. Also use when the user mentions "SEO audit," "technical SEO," "why am I not ranking," "SEO issues," "on-page SEO," "meta tags review," or "SEO health check." For building pages at scale to target keywords, see programmatic-seo. For adding structured data, see schema-markup.

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React composition patterns that scale. Use when refactoring components with boolean prop proliferation, building flexible component libraries, or designing reusable APIs. Triggers on tasks involving compound components, render props, context providers, or component architecture. Includes React 19 API changes.

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Scalingo is a European (French) Platform-as-a-Service for deploying and operating web applications, background workers, and managed databases. Use this skill whenever the user mentions Scalingo, wants to deploy an app to Scalingo, work with the scalingo CLI, provision addons (PostgreSQL, MySQL, MongoDB, Redis, OpenSearch, InfluxDB), configure review apps, manage the scalingo.json manifest or a Procfile, scale containers, set up log drains, migrate from Heroku, use the Scalingo Terraform provider, or target sovereign regions (osc-fr1, osc-secnum-fr1 on SecNumCloud infrastructure). Also trigger for "deploy a French PaaS", "HDS-compliant hosting", "SecNumCloud deployment", or questions about Scalingo's Heroku-compatible buildpack model.

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Explore a flow or layout with 3+ disposable lo-fi greyscale wireframes on a named axis. Use when the user wants to sketch directions or explore structure.

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Geração estruturada rápida e serving para LLMs com RadixAttention para cache de prefixos. Use para saídas JSON/regex, decodificação restrita, workflows com agentes que fazem chamadas de ferramentas, ou quando você precisa de 5× mais rápido que vLLM com compartilhamento de prefixos. Alimenta 300.000+ GPUs na xAI, AMD, NVIDIA e LinkedIn.

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Treina modelos de linguagem grandes (2B-462B de parâmetros) usando NVIDIA Megatron-Core com estratégias avançadas de paralelismo. Use ao treinar modelos >1B de parâmetros, precisar de máxima eficiência de GPU (47% MFU em H100), ou necessitar de paralelismo tensor/pipeline/sequência/contexto/expert. Framework pronto para produção usado em Nemotron, LLaMA, DeepSeek.

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Use when designing, redesigning, or improving a frontend interface in Angular, React, or Blazor. Use for landing pages, dashboards, components, forms, and responsive layouts that must work mobile-first and then scale to desktop.

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SOP for structured documentation lifecycle. Trigger when: - Designing, writing, reviewing, or auditing large-scale documentation structures. - Navigating phases: Audit, Plan, Draft, Review, Verify. - Prompt contains: /doc, doc workflow, audit, draft, review, verify, documentation debt.

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