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概要と使いどころ
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.
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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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Implements missing-data sensitivity analyses for confirmatory clinical trials including MMRM under MAR (with Kenward-Roger correction), reference-based multiple imputation (J2R, CR, CIR, LMCF per Carpenter-Roger 2013), Permutt delta-adjustment / tipping-point analysis, pattern-mixture identifying restrictions (CCMV, NCMV, ACMV), and the Cro vs Bartlett variance debate. Use when handling missing primary or secondary endpoint data in regulatory submissions following NRC 2010 and ICH E9(R1).
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Detects allele-specific transcription factor or histone modification binding from heterozygous-variant ChIP-seq using WASP (reference-bias filter; mandatory upstream), RASQUAL (joint QTL + bias-corrected testing), BaalChIP (Bayesian beta-binomial with copy-number-aware overdispersion), and AlleleSeq (personalized diploid genome). Handles imprinted-locus awareness, X-inactivation artifacts, cancer copy-number imbalance, and integration with downstream caQTL / bQTL mapping. Use when identifying variants with allelic effects on TF binding, fine-mapping causal regulatory variants, validating deep-learning variant predictions, or characterizing cis-acting regulatory effects.
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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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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.
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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.
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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.
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Analyzes alternative splicing from PacBio Iso-Seq (HiFi, Kinnex/MAS-Iso-seq) and Oxford Nanopore (direct cDNA, direct RNA, R10.4.1+) long-read RNA-seq with full-isoform resolution. Tools include FLAIR (correct/collapse/quantify/diffSplice for PacBio + ONT), IsoQuant (de-novo or annotation-guided isoform discovery 2024 SOTA), Bambu (annotation-aware Bayesian discovery + quantification with Novel Discovery Rate), SQANTI3 (isoform classification: FSM/ISM/NIC/NNC + artifact flags), rMATS-long (event calling on long-read isoforms), and minimap2 (-ax splice:hq for HiFi; -ax splice -k14 for ONT cDNA; add -uf only for direct RNA or stranded cDNA preps). Solves microexon detection, recursive splicing, complex multi-exon isoforms, and DTU without transcript-quantification uncertainty. Use when short-read AS limitations (anchor length, complex isoforms, microexons, recursive splicing, transcript ambiguity) demand full-isoform resolution.
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Configures and enforces SwiftLint in Swift projects using build tool plugins, run scripts, and CI. Covers .swiftlint.yml configuration, disabled_rules, opt_in_rules, only_rules, analyzer_rules, baselines, autocorrect, swiftlint:disable suppressions, reporter formats (sarif, json, checkstyle), strict and lenient modes, SwiftLintBuildToolPlugin via SimplyDanny/SwiftLintPlugins, swift package plugin swiftlint, Xcode run script phases, CI integration, multiple configuration files, and rollout strategies for existing codebases. Use when setting up SwiftLint, configuring lint rules, suppressing warnings, creating baselines, choosing between build tool plugin and run script, or integrating SwiftLint into CI.
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Formats and parses locale-aware numbers, decimals, currencies, percentages, dates, durations, measurements, names, lists, byte counts, and URLs with Foundation FormatStyle and ParseableFormatStyle. Use when replacing legacy Formatter subclasses, designing reusable format APIs, using SwiftUI Text(_:format:), correcting availability, or testing user-facing formatted output across locales.
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Builds and reviews SwiftUI views with modern MV architecture, state, composition, isolated previews, and migration guidance. Covers @Observable ownership, @State/@Bindable/@Environment wiring, view decomposition, ViewModifiers, environment values, .task loading, iOS 26+ handoffs, Writing Tools, clipboard availability, and performance. Use when structuring SwiftUI state, managing @Observable, composing views, previewing meaningful UI states, or correcting SwiftUI patterns.
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Implement, review, or improve localization and internationalization in iOS/macOS apps — String Catalogs (.xcstrings), generated localizable symbols, stable key naming, LocalizedStringKey, LocalizedStringResource, pluralization, FormatStyle for numbers/dates/measurements, right-to-left layout, Dynamic Type, and locale-aware formatting. Use when adding multi-language support, setting up String Catalogs, enabling generated symbols for compile-time-safe localization keys, handling plural forms, formatting dates/numbers/currencies for different locales, testing localizations, or making UI work correctly in RTL languages like Arabic and Hebrew.
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This skill should be used when the user asks to "simplify", "clean up the diff", "run simplify", "simplify the changes", "review changed code for cleanup", explicitly invokes "/simplify", or asks to "commit without simplify", "skip simplify for this commit", or "commit this but skip simplify". Reviews changed code across reuse, simplification, efficiency, and altitude, or grants an explicit one-commit bypass. Not for correctness bugs.
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Deploys and operates a LiveKit agent in production: shipping a version to LiveKit Cloud and rolling it back, secrets and configuration, the worker process model and prewarming, safe async inside worker processes, provider timeouts and degradation, graceful shutdown, SDK upgrades, and observability. Use when the user says "deploy my agent", "roll back the deployment", "tail the agent logs", "the first call after a restart is slow", "attached to a different loop / event loop is closed", "prewarm the VAD", "shut down without dropping calls", "upgrade livekit-agents safely", "correlate logs by session", or is changing an agent codebase that is already live. Not for designing the agent (building-livekit-agents) or reproducing one bad conversation locally (debugging-livekit-agents).
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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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Plan manipulator motion and generate trajectories in MATLAB. Use when the task involves moving a robot arm between configurations or poses — whether the user says "trajectory," "motion," "path," "move from A to B," or "plan." This skill applies regardless of whether the user explicitly mentions collisions or obstacles; if geometry exists in the workspace, collision safety is implicit. Triggers on: manipulatorRRT, manipulatorCHOMP, dlCHOMP, contopptraj, trapveltraj, collision-free path, motion planner, RRT, CHOMP, TOPPRA, path shortening, obstacle avoidance for manipulators, time-optimal trajectory, velocity limits, acceleration limits, occupancyMap3D, meshtsdf, collision objects as environment, trajectory between waypoints, joint interpolation, move between poses, constant velocity, trapezoidal profile, feed rate. Also triggers when a user has IK solutions or waypoints and needs to connect them — whether for time-optimal motion, constant-speed welding/cutting, or any other trajectory parameterization.
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Generate correct MATLAB code using the Symbolic Math Toolbox. Use when the user asks for symbolic computations, analytical solutions, symbolic differentiation/integration, equation solving, or converting symbolic results to numeric MATLAB functions. Also use when converting differential equations to transfer functions or state-space form, extracting PDE coefficients (pdeCoefficients), symbolic-to-C code generation (matlabFunction + codegen), symbolic matrix variables (symmatrix), physical units and constants (symunit, newUnit), or rewriting/combining algebraic expressions (rewrite, combine).
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Guide users or agents to the correct MATLAB tool for processing large tabular data in file-based formats (CSV, Parquet, delimited text, spreadsheets, MDF) that may not fit in memory. Use when a user or agent mentions large files, big data, out-of-memory errors, OOM, scaling up, tall arrays, datastores, or needs to process multiple tabular files. Covers the decision between datastore + tall, datastore + transform, and parallel execution. Also use when a user or agent has working in-memory code (readtable, parquetread) that runs out of memory and needs a migration path. Also covers building custom datastore classes for proprietary or non-standard formats — use when the task requires subclassing matlab.io.Datastore, implementing a custom reader, building an extensible datastore, or integrating a new file format with tall arrays or parallel computing. Do NOT use for MAT files (use matfile instead).
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Register 3-D point clouds using ICP, NDT, LOAM, FGR, phase correlation, and CPD algorithms. Use when registering or aligning 3-D point clouds, choosing a registration algorithm, tuning registration parameters, preprocessing point clouds for registration or combining point clouds after registration.
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Build machine vision inspection systems with MATLAB Visual Inspection Toolbox. Covers the full arc from problem selection through deployment: anomaly detection (Student-Teacher, PatchCore, FastFlow, FCDD), object detection (YOLOX), counting (CounTR, shape matching), gauging and measurement (caliper, fitcircle, fitangle), blob analysis (regionprops, calibrated measurement), shape matching for fixturing and localization, synthetic data generation for training augmentation, and deployment to standalone apps, embedded C/C++, NVIDIA GPUs (TensorRT), NPUs (ONNX), and Beckhoff PLCs. Routes to rule-based tools when problems are geometric and deterministic, AI-based tools when defect appearance varies, and hybrid pipelines combining both.
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Share MATLAB content by guiding users through uploading to GitHub, MATLAB Drive, or File Exchange, then generating "Open in MATLAB Online" URLs. Covers the full sharing workflow: choosing a platform, uploading content (automated via gh CLI for GitHub, manual for MATLAB Drive and File Exchange), and constructing the correct URL. Use when a user wants to share MATLAB code with others, open local files in MATLAB Online, generate an open-in-MATLAB-Online button or badge, or when an AI agent has generated MATLAB code locally and the user wants to share it or run it in MATLAB Online.
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Reviews MATLAB fixed-point (fi) code for performance, code generation efficiency, and correctness. Identifies antipatterns and suggests idiomatic improvements. Use when reviewing fi, fimath, numerictype, or quantizenumeric code.
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