기타 스킬

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

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Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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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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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or detecting reference allele mapping bias before downstream analysis.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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Use when the user mentions App Store screenshot validation, screenshot review, checking screenshots before submission, or verifying screenshot dimensions and content.

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Use when accepting ANY real-world payment — Apple Pay, Wallet passes, Tap to Pay, Orders in Wallet. NOT in-app purchase / digital content (use axiom-integration). Covers entitlements, certs, signing, App Review payment rules.

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Use when the user has a crash log (.ips, MetricKit JSON, legacy .crash text, .xccrashpoint bundle, or pasted text) that needs analysis.

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Use when working with ANY GPU rendering, Metal, OpenGL migration, shaders, 3D content, RealityKit, AR, USD/USDZ files, or display performance. Covers Metal migration, shader conversion, RealityKit ECS, RealityView, USDKit, ProMotion.

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Use when the user wants to triage a CORPUS of production crashes/hangs from an aggregator (Sentry, App Store Connect) — grouped, counted issues — rather than a single crash file.

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Use when the user wants to add in-app purchases, implement StoreKit 2, or set up subscriptions.

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Use when the user mentions slow builds, build performance, or build time optimization.

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Implement, review, or improve WidgetKit widgets and controls. Use when building Home Screen, Lock Screen, StandBy, or CarPlay widgets with timeline providers; configurable widgets with AppIntentTimelineProvider; interactive widgets or Control Center controls with Button/Toggle wiring; WidgetKit push reloads, refresh budgets, deep links, Smart Stack relevance, Liquid Glass/accented rendering, widget extension setup, WidgetBundle, App Groups, and entitlements.

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Create child communication safety experiences using PermissionKit to request parental permission for children. Use when building apps that involve child-to-contact communication, need to check communication limits, request parent/guardian approval, or handle permission responses for minors.

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Build alternative browser engines using BrowserEngineKit. Use when developing a non-WebKit browser engine for iOS/iPadOS in supported regions, managing web content/rendering/networking extension processes, configuring GPU and networking process capabilities, checking alternative-engine device eligibility, or reviewing BrowserEngineKit entitlements and Info.plist setup.

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Read and write NFC tags using CoreNFC. Use when scanning NDEF tags, reading ISO7816/ISO15693/FeliCa/MIFARE tags, writing NDEF messages, handling NFC session lifecycle, configuring NFC entitlements, or implementing background tag reading in iOS apps.

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Implement, review, or improve Live Activities and Dynamic Island experiences in iOS apps using ActivityKit. Use when building real-time updating widgets for the Lock Screen and Dynamic Island — delivery tracking, sports scores, ride-sharing status, workout timers, media playback, or any time-sensitive information that updates in real time. Also use when working with ActivityKit, ActivityAttributes, Activity lifecycle (request/update/end), Dynamic Island layouts (compact/minimal/expanded), push-to-update Live Activities, or Lock Screen live widgets.

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Query grid electricity forecasts and submit load events using EnergyKit to help users optimize home electricity usage. Use when building smart home apps, EV charger controls, HVAC scheduling, or energy management dashboards that guide users to use power during cleaner or cheaper grid periods.

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Integrate Apple Pay payments and Wallet passes using PassKit. Use when adding Apple Pay buttons, creating payment requests, handling payment authorization, adding passes to Wallet, configuring merchant capabilities, managing shipping/contact fields, or working with PKPaymentRequest, PKPaymentAuthorizationController, PKPaymentButton, AddPassToWalletButton, PKPass, PKAddPassesViewController, PKPassLibrary, Wallet pass distribution, or Apple Pay checkout flows for physical goods, real-world services, donations, and eligible recurring payments.

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