「vc」の検索結果

Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region traps, trio phasing as the gold standard, and the boundary to statistical panel phasing. Use when phasing long-read variants, haplotagging reads for allele-specific methylation/expression or phased SVs, choosing WhatsHap vs LongPhase vs HiPhase, trio phasing, or assessing phasing quality.

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。

Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged conversion, the silent failures (chrom-name mismatch, CRLF, lexicographic-vs-version sort under -sorted), genome/chrom.sizes generation, sorting contracts, BED12 block invariants, validation, makewindows, cross-assembly liftover (liftOver/CrossMap), and BED<->VCF/BAM/FASTA conversion. Use when reading, creating, validating, sorting, lifting between genome builds, or converting interval files, preparing inputs for bedtools/tabix/bigBed, or debugging an off-by-one or empty-overlap result.

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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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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.

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Use when working with camera, photos, audio, haptics, ShazamKit, on-device music analysis, face grouping and video highlights, screen recording, casting to non-AirPlay routes, SharePlay playback, the user's Apple Music library, lock-screen metadata, or CarPlay app design, templates, and navigation. Covers AVCaptureSession, AVFoundation, Core Haptics, MediaPlayer, MusicKit, NowPlaying, ScreenCaptureKit, DockKit.

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Implement, review, or improve photo picking, camera capture, and media handling in iOS apps using PhotoKit and AVFoundation. Use when working with PhotosPicker, PHPickerViewController, camera capture sessions (AVCaptureSession), photo library access, image loading and display, video recording, or media permissions. Also use when selecting photos from the library, taking pictures, recording video, processing images, or handling photo/camera privacy permissions in Swift apps.

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Model a Phase-Locked Loop (PLL) IC from its datasheet or system specs using Mixed-Signal Blockset. Without this skill, agents universally select the wrong solver and produce non-functional PLL models — 100% of unguided attempts fail. Covers Integer-N, Fractional-N, Dual Modulus architectures, loop filter design, lock time optimization, VCO phase noise configuration, and msbPllArchitectures/msbPllFoundation block assembly. Use when: PLL modeling, frequency synthesizer design, phase noise simulation, lock time analysis, charge pump design, loop filter tuning, datasheet-to-model, Mixed-Signal Blockset PLL, msbPllArchitectures.

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Analyze AMS waveform data using Mixed-Signal Blockset utilities: phase noise measurement, clock jitter, anti-aliased resampling, timing measurements, lock time, INL/DNL, ADC/DAC calibration, HSpice import. Use when analyzing time-domain voltage from PLL/VCO/clock simulations, measuring phase noise from variable-step solver output, computing jitter, or resampling non-uniform data.

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Create reproducible development environments with Dev Containers, Nix flakes, and Devbox for consistent toolchains across teams. Use when onboarding developers, standardizing build environments, or eliminating "works on my machine" problems.

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Create or update implementation plans in the repo's SIMPLE or COMPLEX format. Use when turning an idea, PRD, or approved direction into a saved plan artifact.

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Apply step-by-step analysis for complex problems with revision capability. Use for multi-step reasoning, hypothesis verification, adaptive planning, problem decomposition, course correction.

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AI-optimized browser automation CLI with context-efficient snapshots. Use for long autonomous sessions, self-verifying workflows, video recording, and cloud browser testing (Browserbase).

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Emit and validate the provisional goal block for Autopilot Mode. Owns the 9-field format and resume detection from a pasted goal block.

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Generate kickoff artifacts for a multi-phase program: umbrella plan, Program Goal Charter, session-goal block, per-phase plan stubs, and the 7-step per-phase inner loop reference.

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Clarify intent before RIPER-5 phase delegation. Scores ambiguity (4 signals); generates structured multi-choice questions for Tier 2. Two-mode: SIMPLE and DEEP.

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Fast codebase scouting using shell search and optional parallel research agents. Use for file discovery, task context gathering, and quick scoped searches across directories.

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Search library/framework documentation via llms.txt (context7.com). Use for API docs, GitHub repository analysis, technical documentation lookup, latest library features.

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Use when a SPEC, INNOVATE, or VALIDATE (Layer 2) approach hinges on an unverified runtime/library/external mechanism: run a probe from the 8-family taxonomy and produce a VIABLE/NOT-VIABLE/INCONCLUSIVE VERDICT artifact.

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Generate the post-EXECUTE closeout packet for a plan or phase. Includes archive-readiness classification, drift signal scoring, commit checkpoint recommendation, and move-on next-state recommendation.

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Audit active project plan files for staleness, completion, and routing truth. Use when cleaning up plans, reconciling active work, or archiving completed artifacts.

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Apply systematic problem-solving techniques when stuck. Use for complexity spirals, innovation blocks, recurring patterns, assumption constraints, simplification cascades, scale uncertainty.

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5 expert personas debate proposed changes before implementation. Catches architectural, security, performance, and UX issues early. Use before major features or risky changes.

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Web testing with Playwright, Vitest, k6. E2E/unit/integration/load/security/visual/a11y testing. Use for test automation, flakiness, Core Web Vitals, mobile gestures, cross-browser.

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。