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Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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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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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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Extracts and assigns COSMIC v3.4 mutational signatures (86 SBS / 11 DBS / 18 ID / 21 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF, SigNet, or HRDetect. Use when characterizing DNA-damage etiology (BRCA1/2 HRD, MMR-D, POLE, APOBEC3A, UV, tobacco, aflatoxin, 5-FU/SBS17b, platinum, colibactin SBS88), routing PARP inhibitor decisions, or auditing de novo extraction vs refit choice for cohort size.

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Queries PharmGKB / CPIC / DPWG for drug-gene interactions; calls CYP2D6/CYP2C9/CYP2C19/DPYD/TPMT/NUDT15/UGT1A1/SLCO1B1 star alleles and phenotype with PharmCAT, Cyrius (CYP2D6 structural variants), Aldy, Stargazer; applies Caudle 2020 activity-score translation. Use when implementing pharmacogenomic-guided prescribing, applying CPIC vs DPWG guidance, screening HLA risk alleles for ICI / antiepileptics / abacavir, or interpreting compound TPMT+NUDT15 thiopurine risk.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

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Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible.

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Use when building ANY 2D or 3D game with SpriteKit, SceneKit, or RealityKit, or adding touch controls or game controller support. Covers scene graphs, ECS, physics, actions, game loops, rendering, TouchController, GCController.

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Use when the user wants to audit SpriteKit game code for common issues — physics bitmask issues, draw call waste, node accumulation, and action leaks.

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Use when the user mentions in-app purchase review, IAP audit, StoreKit issues, purchase bugs, transaction problems, or subscription management.

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Use when making visual or interaction design decisions for an Apple app — HIG patterns, Liquid Glass, SF Symbols, typography, app entry-point and auth-flow structure.

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Build 2D games and animations using SpriteKit. Use when creating game scenes with SKScene and SKView, adding sprites with SKSpriteNode, animating with SKAction sequences, simulating physics with SKPhysicsBody and contact detection, creating particle effects with SKEmitterNode, building tile maps, using SKCameraNode, or integrating SpriteKit scenes in SwiftUI with SpriteView.

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Build SwiftUI layouts using stacks, grids, lists, scroll views, forms, and controls. Covers VStack/HStack/ZStack, LazyVGrid/LazyHGrid, List with sections and swipe actions, ScrollView with ScrollPosition and scroll-driven reveal surfaces, Form with validation, Toggle/Picker/Slider, .searchable, and overlay patterns. Use when building data-driven layouts, collection views, paged detail reveals, settings screens, search interfaces, or transient overlay UI.

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Maintain and extend existing SceneKit 3D scenes and visualizations. Use when working with SCNView, SCNScene, SCNNode scene graphs, SceneKit geometry/materials/lights/cameras, SCNAction animation, SCNPhysicsBody physics, SCNParticleSystem effects, .scn/.dae/.abc SceneKit assets, shader modifiers, or SwiftUI SceneView. SceneKit is soft-deprecated and in maintenance mode; route new apps, significant updates, USD/USDZ pipelines, and migration planning toward RealityKit.

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Build iOS augmented reality and 3D experiences with RealityKit and ARKit. Use when adding RealityView content, loading entities or USDZ models, anchoring objects to planes or world positions, distinguishing entity hit tests from ARKit real-world raycasts, handling AR camera availability, world tracking, scene updates, or RealityKit entity gestures and interactions.

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Implement and review Apple TipKit feature-discovery UI for iOS 17+ apps. Use when adding or auditing in-app tips, contextual help, coach marks, Tip, TipView, popoverTip, rules, events, actions, display frequency, testing overrides, reusable tip identifiers, or iOS 18+ TipGroup and CloudKit tip sync; avoid for generic SwiftUI navigation or layout outside tip presentation.

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Access Core Motion accelerometer, gyroscope, magnetometer, device-motion, pedometer, activity-recognition, altitude, headphone motion, batched high-frequency workout motion, and water-submersion/depth data. Use when reading device sensors, counting steps, detecting walking/running/driving/cycling, tracking altitude, building motion interactions, handling AirPods head tracking, or implementing watchOS dive/depth features.

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Implements keyboard, directional, and scene-level focus behavior across SwiftUI and UIKit. Use when managing @FocusState, defaultFocus, focused values, focusable interactions, focus sections, tvOS geometric focus and Siri Remote navigation, watchOS Digital Crown input, visionOS connected-device focus versus gaze hover/input targets, macOS key view loop and Full Keyboard Access, focus restoration after presentation changes, custom focus routing with UIFocusGuide, or debugging focus with UIFocusDebugger.

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Implement AlarmKit alarms and countdown timers for iOS and iPadOS with Lock Screen, Dynamic Island, StandBy, and paired Apple Watch system UI. Covers AlarmManager scheduling, AlarmAttributes and AlarmPresentation, system Stop and AlarmButton secondary actions, authorization, state observation, countdown widget-extension handoff, and Live Activity integration. Use when building wake-up alarms, countdown timers, or alarm-style alerts that need Apple's system alarm experience.

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Implement VoIP calling with CallKit and PushKit. Use when building incoming/outgoing call flows, registering for VoIP push notifications, configuring CXProvider and CXCallController, handling call actions, coordinating audio sessions, or creating Call Directory extensions for caller ID and call blocking.

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Optimize App Store product pages for search visibility and conversion. Use for App Store Optimization (ASO), keyword research, app name/subtitle/keyword-field strategy, conversion-focused descriptions and promotional text, screenshot captions and ordering, Custom Product Pages with assigned search keywords, In-App Events, Product Page Optimization tests, localized metadata, ratings/review strategy, and in-app review prompt timing with RequestReviewAction or AppStore.requestReview. Also use when routing ASO vs App Store review, privacy/ATT, or StoreKit implementation boundaries.

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。