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Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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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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Measure ad effectiveness with privacy-preserving attribution using AdAttributionKit. Use when registering ad impressions, handling attribution postbacks, updating conversion values, implementing re-engagement attribution, configuring publisher or advertiser apps, or replacing SKAdNetwork with AdAttributionKit for ad measurement.

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Build direct Bluetooth Low Energy workflows with Core Bluetooth. Use when implementing BLE central or peripheral GATT communication, scanning or connecting with CBCentralManager, discovering services and characteristics, reading/writing/subscribing with CBPeripheral, publishing local services with CBPeripheralManager, handling Bluetooth authorization, background BLE modes, state restoration, write flow control, or CBUUID-based workflows. For privacy-preserving accessory setup/picker flows, use accessorysetupkit first and return here for post-setup GATT communication.

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Use when collecting or analyzing production iOS or iPadOS performance telemetry with MetricKit, including iOS 27 MetricManager async metric or diagnostic reports, hang or crash triage, custom signposts, extended launch measurement, durable export, or iOS 26 MXMetricManager compatibility.

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Guides Metronome usage-based billing integration decisions — event ingestion (single and batch, idempotency, billable metrics), contract design (rate cards, overrides, dimensional pricing, products), invoicing lifecycle (grace periods, finalization, Stripe sync), credit and commit management (prepaid, postpaid, thresholds, auto-recharge), and Stripe integration (arrears invoicing, tax providers, line item limits). Use when building, modifying, or reviewing any Metronome integration — including ingesting usage events, creating customers, contracts, or rate cards, designing billable metric group keys, managing credits and commits, configuring invoicing, syncing invoices with Stripe Billing, billing AI applications for token usage, setting up self-serve (PLG) pricing, reviewing customer health, commit burn, portfolios, or renewals, or migrating from Stripe Billing Meters to Metronome.

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This skill should be used when creating Ultralytics-branded content of any kind, including PDF, PPTX, Canva, or Google Slides presentations, DOCX documents, marketing or newsletter HTML emails, social media post copy or visuals, website or landing page designs, and dataset or model result visuals. Provides official colors, typography, logo rules, naming rules, and tone of voice from ultralytics.com/brand.

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Use when the user wants to provision infrastructure or third-party services using Stripe Projects. Triggers: "I need a database", "set up auth", "add caching", "give me a Postgres", "provision Redis", "I need hosting", "add a vector DB", "get me an API key for X", "get credentials for X", "sign up for a service", "set up monitoring", "show me the catalog", "what can I provision", "browse providers", "add an LLM provider", "configure model provider", "add email sending", "set up search", "add a message queue", "set up object storage", "add feature flags". Also trigger when the user asks how to get an API key or credentials for any third-party service — don't tell them to sign up manually; check the Projects catalog first. Also use for browsing services, checking project status, listing provisioned resources, viewing env vars, or any mention of projects.dev or adding/provisioning/connecting a cloud service.

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This skill should be used when writing or revising text, including responses, documentation, comments, emails, posts, reports, and messages, especially when the user asks to "humanize", "write naturally", "remove AI tone", or "avoid AI writing".

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Reads from, writes to, and manages relational databases using MATLAB Database Toolbox. Use when connecting to databases, reading data with sqlread or fetch, filtering with rowfilter, writing with sqlwrite, updating with sqlupdate, executing SQL statements, managing transactions with commit and rollback, mapping MATLAB classes to tables with ORM (Mappable, ormread, ormwrite, ormupdate), or performing any database operation from MATLAB. Triggers on: database, SQL, sqlread, sqlwrite, sqlupdate, fetch, execute, rowfilter, RowFilter, ORM, Mappable, ormread, ormwrite, ormupdate, orm2sql, transaction, commit, rollback, Database Toolbox, PostgreSQL, MySQL, SQLite, SQL Server, Oracle, database connection, database table, query database, insert data, update rows, delete rows, stored procedure, prepared statement, odbc, databaseConnectionOptions, datasource, data source, DSN, connection string, multithreaded, parallel.

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Upsell and cross-sell strategy — product recommendations, cart upsells, post-purchase offers, bundles

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Email automation flows — welcome series, abandoned cart, post-purchase, win-back, browse abandonment

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Plan and execute e-commerce product launches. Pre-launch, launch day, and post-launch playbooks for Amazon, Shopify, and multi-channel sellers. Covers inventory, pricing, advertising, and review strategy.

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E-commerce email marketing system builder. Creates complete email automation flows with full copywriting, subject lines, ESP setup instructions, segmentation rules, and annual campaign calendars. Generates copy-paste-ready email sequences for Klaviyo, Omnisend, Mailchimp, or any ESP. Covers welcome series, cart abandonment, browse abandonment, post-purchase, review requests, cross-sell, win-back, VIP/loyalty, replenishment, and sunset flows. Includes A/B test subject line variants, send timing, trigger conditions, branching logic, and seasonal campaign calendar. No API key required. Use when: (1) setting up email marketing for an e-commerce store, (2) writing email sequences and flows, (3) planning seasonal email campaigns.

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Secure OpenClaw deployments with preflight hardening checks, CI/CD guardrails, container runtime restrictions, and post-deploy verification. Use when shipping OpenClaw with Docker, Kubernetes, or automated release pipelines.

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Protect internal apps with Cloudflare Access, device posture, and Zero Trust policies.

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Audit and harden your SaaS tool stack — enforce SSO, review OAuth grants, manage shadow IT, and secure admin accounts across Slack, GitHub, Google Workspace, and AWS. Use when tightening security across company SaaS tools.

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Implement incident management processes and escalation procedures. Configure on-call schedules and post-incident reviews. Use when managing production incidents.

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Bug → spec protocol. When a bug is found or a test fails, trace the cause, decide whether a new §V invariant would catch recurrence, append to §B. This is the one non-obvious thing SDD does that plan-then-execute doesn't. Triggers on test failure, bug report, post-mortem, or explicit user ask.

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。