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Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction between within-run drift correction and between-batch correction, the mandatory anchor/reference sample, why normalization is per-cluster with many quantiles, and the over-correction risk. Use when correcting CyTOF signal drift, harmonizing multi-batch or multi-site studies, or deciding whether to normalize data versus model batch in the design.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.

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Runs JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens; Allen et al 2019 Genome Research) which models per-sgRNA log-fold-change as the product of a treatment-dependent gene-essentiality term and a treatment-independent guide-efficacy term. Covers the Bayesian decomposition math, the hierarchical efficacy prior shared across screens performed with the same library, when JACKS outperforms MAGeCK (multi-screen joint analysis, libraries with broad efficacy variance) and when it does not (single screen, novel libraries with no prior efficacy), library-reuse efficacy transfer, downstream essentiality interpretation, and the 2.5x sample-size reduction enabled by efficacy-aware testing. Use when running multiple screens with the same library, when guide-level noise is suspected to dominate per-gene signal, when reusing published essentiality reference screens for efficacy priors, or when comparing screens performed across cell lines that share library but differ biologically.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract) with SES scaling, k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, MultiSuSiE, and FOCUS. Use when narrowing a GWAS lead SNP to a 95 percent credible set, choosing between in-sample and reference LD, calibrating non-sparse loci with SuSiE-inf or FINEMAP-inf, integrating functional priors via PolyFun, fine-mapping across ancestries with SuSiEx, diagnosing LD mismatch via estimate_s_rss and kriging_rss, handling HLA or long-range LD, or feeding credible sets into coloc.susie for colocalization.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiotropy and choosing among Egger, MR-PRESSO, MR-RAPS, CAUSE, LHC-MR, LCV, MR-Clust, MR-Mix, and contamination-mixture methods. Use when validating an MR causal claim, running the STROBE-MR sensitivity battery, suspecting a shared heritable confounder, working under weak-instrument or polygenic-exposure regimes, or reconciling discordant estimates across robust methods.

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Use when capturing or analyzing ETTrace profiles for a focused iOS launch or runtime flow, including exact-build dSYM UUID matching, Simulator or device capture, processed per-thread flamegraph JSON, sampled inclusive/exclusive time, unresolved symbols, and comparable verification. Use debugging-instruments or swiftui-performance for generic profiling instead.

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Generate read-only MongoDB queries (find) or aggregation pipelines using natural language, with collection schema context and sample documents. Use this skill whenever the user asks to write, create, or generate MongoDB queries, wants to filter/query/aggregate data in MongoDB, asks "how do I query...", needs help with query syntax, or discusses finding/filtering/grouping MongoDB documents. Also use for translating SQL-like requests to MongoDB syntax. Does NOT handle Atlas Search ($search operator), vector/semantic search ($vectorSearch operator), fuzzy matching, autocomplete indexes, or relevance scoring - use search-and-ai for those. Does NOT analyze or optimize existing queries - use mongodb-query-optimizer for that. Does NOT handle aggregation pipelines that involve write operations. Requires MongoDB MCP server.

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Generate Bluetooth Low Energy (BLE) PHY waveforms. Read BEFORE writing any BLE waveform code to avoid hallucinating API patterns. Covers bleWaveformGenerator, bleIdealReceiver, bleCTEIQSample, bleAngleEstimate, bluetoothTestWaveform for LE1M/LE2M/LE500K/LE125K. Bluetooth Toolbox R2022a+.

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Set up and run wireless network simulations using the Wireless Network Toolbox. Use this skill when creating system-level simulations with wirelessNetworkSimulator, adding traffic sources (networkTrafficOnOff, networkTrafficFTP, networkTrafficVoIP, networkTrafficVideoConference), configuring node mobility, logging events or IQ samples, visualizing traffic, scheduling actions during simulation, running parametric sweeps, writing PCAP files with pcapWriter or technology-specific PCAP writers, registering event callbacks on wireless nodes, accessing event data fields, or combining multiple capture/visualization tools in a simulation.

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Set up and verify a connection to an NI USRP radio (USRP E320, N300, N310, N320, N321, X300, X310, or X410) using Wireless Testbench. Use when connecting a USRP for the first time, configuring radio hardware, troubleshooting connection failures, or verifying a radio setup. Covers host inspection (OS, NIC type/speed/MTU), device discovery (findsdru, probesdru), UHD version checking, programmatic radio configuration, and basebandTransceiver verification. Also use when the user mentions USRP setup, radio not found, connection errors, dropped samples, or network configuration for SDR hardware.

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Translate NI-DAQmx C function signatures into correct calldaqlib MATLAB calls. Use when the user mentions calldaqlib, any DAQmx* C function name (DAQmxCfgSampClkTiming, DAQmxExportSignal, DAQmxSetStartTrigRetriggerable, DAQmxGetSampClkRate, etc.), or needs NI-DAQmx functionality not exposed by the daq object. Covers: projection rules (taskHandle implicit, output pointers become return values, buffer-size args, enum-as-string), multi-task semantics, start() clobber, device-level empty-daq workaround, dictionary returns, string getter placeholder, array getter placeholder. Trigger contexts: low-level DAQ, escape hatch, retriggerable acquisition, shared timebase, export signal, connect terminals, external sample clock, trigger configuration, NI driver, C function translation.

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Use when designing a Digital Down Converter (DDC) using dsphdl System objects. Triggers on requests involving DDC design, frequency down-conversion for FPGA/ASIC, NCO + mixer + decimation filter chains, fractional/non-integer sample rate conversion, or HDL-optimized receiver front-end signal processing.

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Design and implement real-time audio processing chains using Audio Toolbox streaming objects. Use when building frame-based audio processing loops, multiband filters, dynamic range control, parametric EQ, level metering, loudness metering, SPL metering, octave-band analysis, sample rate conversion, frequency-domain filtering (long impulse responses, custom filter banks), or audio chains in Simulink. Covers visualization (visualize method), interactive tuning (parameterTuner), MIDI control, and Audio Toolbox Simulink blocks. Use when the user says "real-time audio", "streaming audio", "audio filter", "compressor", "equalizer", "level meter", "loudness meter", "SPL meter", "octave bands", "crossover filter", "audio chain", "MIDI control", "convolution reverb", "impulse response streaming", "frequency-domain filter", or asks to process audio frame-by-frame.

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TikTok Shop affiliate program strategy and creator collaboration. Commission structures, creator recruitment, sample management, performance tracking, and partnership optimization. Use when the user asks about TikTok Shop affiliates, creator partnerships, or TikTok Shop Creator Fund.

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Plan, build and quality-check a premium short commercial for a real business (roofing, property, ecommerce, B2B software) using AI-generated footage, code-built motion (HTML/GSAP), selective Three.js and an independent-critic "Gauntlet" loop. Use when asked to make a launch-style / SaaS-style video, business ad, explainer, sample reel or pitch video, or to review and improve one. Encodes motion principles distilled from 28 professional launch films, a quality bar, audio rules and a business-offer playbook.

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Set up Vitest testing in any project — detects type (Cloudflare Workers, React, Node, library), generates vitest.config.ts, test setup, utilities, and a sample test. Covers mocking patterns, coverage config, workspace setup, Jest migration. Use whenever the user mentions adding tests, setting up Vitest, configuring tests, migrating from Jest, fixing testing infrastructure, or asks 'how do I test this'.

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Use when generated assets must keep a consistent style, character, or product look and references stop scaling, or when a user asks to train a custom model through the Scenario MCP, fine-tune a LoRA, clone a voice, curate a training dataset, choose a base model, set epochs and sample prompts, estimate training cost, diagnose a trained model that lost its identity or has one epoch, or generate with a trained model. Keywords: custom model, LoRA, dataset curation, epoch previews.

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How to read experiment results without fooling yourself. Confidence intervals, p-values, multiple testing, sequential testing, CUPED, heterogeneous treatment effects, ratio metrics, network effects, dashboard reconciliation, and the interpretation failures that produce confidently wrong shipping decisions. Use this skill whenever the user is reading a finished experiment result panel and about to make a ship, kill, or iterate decision, or when an experiment number does not match the dashboard number. Triggers on read experiment results, result panel, ship or kill decision, p-value, confidence interval, statistical significance, multiple testing, peeking, sequential testing, CUPED, variance reduction, heterogeneous treatment effects, ratio metric, network effects, inconclusive test, experiment versus dashboard mismatch. Use `experiment-design` instead when the test has not run yet and the question is hypothesis, sample size, duration, or what to test.

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