データ・AIのスキル

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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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.

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Computes sample size and power for clinical trials including continuous, binary, and time-to-event endpoints; superiority, non-inferiority, and equivalence designs; FDA 2016 non-inferiority margin selection with M1/M2 framework; Schoenfeld 1981 and Lakatos 1988 for survival; Schuirmann TOST and 80-125% bioequivalence; minimum clinically important difference (MCID) vs δ distinction. Use when justifying trial size in protocol or SAP per CONSORT 2025 item 16a.

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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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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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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.

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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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Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.

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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

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Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.

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Process and analyze single-cell ATAC-seq data with Signac, ArchR, SnapATAC2, or Cell Ranger ATAC. Use when handling 10X scATAC or 10X Multiome (paired RNA+ATAC) data, performing per-cell QC, choosing between ArchR/Signac/SnapATAC2 ecosystems, building per-cluster consensus peaksets, integrating with paired scRNA-seq, doublet detection (AMULET vs ArchR vs scDblFinder), or running pseudobulk differential accessibility per cluster.

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Use when writing ANY async code, actors, or threads in an Apple-platform app, or seeing ANY concurrency error. Covers Swift 6 concurrency, @MainActor, Sendable, data races, async/await patterns.

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Use when working with ANY data persistence, database, storage, CloudKit, migration, or serialization in an Apple app. Covers SwiftData, Core Data, GRDB, SQLite, Realm, CloudKit sync, file storage, Codable, migrations.

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Use when work crosses into Apple's system surfaces rather than your own UI or data — Siri and Shortcuts, widgets, Live Activities, in-app purchase, localization, privacy prompts, alarms, timers, calendar, reminders, contacts, SharePlay, VoIP and CallKit, accessory pairing, weather, Spotlight indexing, background tasks, Background Assets, push, or push on networks with no internet.

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Implement computer vision features including text recognition (OCR), face detection, barcode scanning, image segmentation, object tracking, and document scanning in iOS apps. Covers both the modern Swift-native Vision API (iOS 18+) and legacy VNRequest patterns, VisionKit DataScannerViewController for live camera scanning, and CoreMLRequest/VNCoreMLRequest for custom model inference. Use when adding OCR, barcode scanning, face detection, or custom Core ML model inference with Vision.

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Fetch WeatherKit current, minute, hourly, and daily forecasts; weather alerts; iOS 18+ changes, historical comparisons, summaries, and statistics; and required Apple Weather attribution. Use when integrating weather data, showing forecasts or alerts, caching WeatherKit responses, displaying attribution, or reviewing WeatherKit query limits in iOS apps.

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Access research-grade sensor data using SensorKit for approved studies. Use when an app needs SensorKit entitlement setup, Research Sensor & Usage Data authorization, ambient light, recorded motion, device usage, keyboard metrics, visits, speech, face, wrist temperature, ECG, PPG, acoustic settings, or sleep-session data. Route ordinary motion to CoreMotion and health records/workouts to HealthKit.

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Tokenize, tag, and analyze natural language text using Apple's NaturalLanguage framework and translate between languages with the Translation framework. Use when adding language identification, sentiment analysis, named entity recognition, part-of-speech tagging, text embeddings, or in-app translation to iOS/macOS/visionOS apps.

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Use Apple CryptoKit for Swift cryptographic primitives. Use when hashing with SHA-2 or SHA-3, generating HMACs, encrypting with AES-GCM or ChaChaPoly, signing with P256/P384/P521/Curve25519 or ML-DSA keys, performing ECDH, HPKE, ML-KEM, or X-Wing key exchange, using Secure Enclave CryptoKit keys, or migrating CommonCrypto code to CryptoKit.

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Read, create, update, and pick contacts using the Contacts and ContactsUI frameworks. Use when fetching contact data, saving new contacts, wrapping CNContactPickerViewController in SwiftUI, handling contact permissions, or working with CNContactStore fetch and save requests.

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