「depth」の検索結果

Prepares for hiring manager rounds at Staff+ (L6+) level — scope of impact, influence without authority, ambiguity navigation, mentorship, strategic thinking. Use when practicing HM rounds or calibrating story depth for target level. Activate on "hiring manager round", "HM screen", "staff level", "scope of impact". NOT for coding interviews, system design, behavioral/values rounds, or resume writing.

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Diagnose and eliminate the GraphQL N+1 resolver explosion using Facebook DataLoader's per-request batching, plus the second-order defenses (persisted queries, depth limits, cost analysis). Use when a GraphQL query that returns N items in a list triggers N+1 database round trips, when designing nested resolvers that load associations, when a list query times out under load, or when you need to budget query cost before resolvers run. NOT for REST-style endpoint design (use api-versioning-strategy), generic database query optimization (use database-query-optimizer), or schema design (use graphql-server-architect).

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Assigns confidence scores to agent outputs based on multiple factors including source quality, consistency, and reasoning depth. Produces calibrated confidence estimates. Activate on 'confidence score', 'how confident', 'certainty level', 'output confidence', 'reliability score'. NOT for validation (use dag-output-validator) or hallucination detection (use dag-hallucination-detector).

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Call germline SNPs and indels with GATK HaplotypeCaller and the GVCF joint-genotyping workflow. Covers the local-reassembly + PairHMM mechanism (why HC beats pileup callers on indels), the -ERC GVCF reference-confidence model and <NON_REF> allele, BQSR-vs-DRAGSTR and --dragen-mode error modeling, allele-specific (AS_) annotations, and edge cases (ploidy, Mutect2 mitochondria mode, sex chromosomes/PAR, contamination gating). Use when deciding whether to use HaplotypeCaller vs a pileup or DRAGEN caller, whether BQSR still earns its place, whether to call per-sample GVCFs for a cohort, or how to handle non-diploid, mitochondrial, sex-chromosome, or contaminated samples. Not for post-calling filtering depth (see variant-calling/filtering-best-practices) or cohort joint-genotyping scaling (see variant-calling/joint-calling).

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Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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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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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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Treats a ctDNA assay as a molecule-counting experiment at the Poisson edge and builds its analytical-validation case the measurement-science way. Covers the genome-equivalent currency (~330 haploid copies/ng), the lambda = input_GE x VAF sampling ceiling (lambda>=3 for ~95% detection), the error-suppression ladder (raw NGS ~1e-3 -> single-strand UMI ~1e-4/1e-5 -> duplex <1e-7), the CLSI EP17 LoB/LoD/LoD95/LoQ framework, the per-locus-vs-panel-integrated LoD distinction that lets bespoke MRD reach ppm, contrived/SEQC2 reference standards, and honest LoD reporting conditioned on input mass + consensus depth + replicate detection rate. Use when stating or trusting a sensitivity claim, designing a dilution-series validation, deciding how many genome equivalents are needed at a target VAF, choosing a single-locus vs panel-integrated LoD, or auditing a "detects 0.1% VAF" claim.

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Expert in building 3D experiences for the web - Three.js, React Three Fiber, Spline, WebGL, and interactive 3D scenes. Covers product configurators, 3D portfolios, immersive websites, and bringing depth to web experiences.

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Practical UI refactoring and visual design review inspired by Refactoring UI by Steve Schoger and Adam Wathan. Use when an AI coding agent needs to improve an existing interface, audit visual polish, redesign a rough UI, review frontend code for hierarchy/spacing/typography/color/depth/image issues, or turn a plain implementation into a cleaner product-quality screen. Do not use for creating UI from scratch, scaffolding a new app, building a new landing page, or designing a new design system unless the user explicitly asks to review or refactor an existing interface.

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Multi-layer validation to catch bugs before they escape

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Research a technical topic thoroughly by exploring the codebase and summarizing findings. Use when asked to investigate how something works, research an area of the codebase, trace a data flow, or understand a component in depth.

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Map existing materials into a first knowledge record, or investigate a subject's history in depth. Use whenever the user asks to map, survey, go through, reconstruct or investigate what already exists - folders of documents, decision records, meeting notes, emails, exports, code - or wants a starting record built from existing materials, even when the word 'record' is never said: consult this before listing or reading the files yourself, because a map has an agreed scope, a protocol and a report. Also, once, at a suitable moment, to offer the starting choices where a workspace has no record and the work is clearly ongoing - never on a greeting. Learning while working needs no map. Requests come in any language.

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Generate architecture and design documents for implemented code changes with risk-based depth selection. Automatically evaluates risk signals, layer spread, and change magnitude to choose documentation level (A/B/C). Use after completing a feature, before merging a PR that touches multiple layers or sensitive areas (auth, infra, migrations, payments), or when an implemented change needs a design record or ADR.

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Use to run a depth-bounded self-correction loop (attempt → critic verdict → re-attempt) as a tunable test-time compute knob — a do-and-judge specialisation, default off, capability-gated.

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Use when validation needs entry, business-logic, environment, and instrumentation guards so a bad value cannot reach the failure point — turns a local bug fix into a structural one.

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Deep analysis of articles/long-form via thinking frameworks (SCQA, mental models, inversion) — 'analyze article', 'deep dive', 'extract insights', URL/text wanting depth not summary.

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Use when the user adds a project to the workspace, opens an unfamiliar repo, asks "what is this project", "explain this codebase", or invokes explain-new-project. Explores a newly opened workspace project and writes a plain-language report for a self-taught, non-technical user—quick start (what it is + how to run) first, then optional depth—and always saves PROJECT_GUIDE.md in the project root.

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Search the web with LLM-optimized results via the Tavily CLI. Use this skill when the user wants to search the web, find articles, look up information, get recent news, discover sources, or says "search for", "find me", "look up", "what's the latest on", "find articles about", or needs current information from the internet. Returns relevant results with content snippets, relevance scores, and metadata — optimized for LLM consumption. Supports domain filtering, time ranges, and multiple search depths.

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Evaluate, rewrite, and select WeChat Official Account article titles for open rate, depth, reader promise, and account tone. Use when drafting, reviewing, publishing, or revising公众号文章标题, especially when titles may be generic, stale, clickbait, AI-flavored, or misaligned with the article's commercial/editorial intent.

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Conduct comprehensive AI-powered research with citations via the Tavily CLI. Use this skill when the user wants deep research, a detailed report, a comparison, market analysis, literature review, or says "research", "investigate", "analyze in depth", "compare X vs Y", "what does the market look like for", or needs multi-source synthesis with explicit citations. Returns a structured report grounded in web sources. Takes 30-120 seconds. For quick fact-finding, use tavily-search instead.

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