「by」の検索結果

Facilitate Kimball-style dimensional (data warehouse / BI) modeling sessions through conversation, producing DimML (Dimensional Modeling Language, YAML) as the primary artifact plus a bus-matrix + star-schema HTML. Use whenever the user wants to design fact tables, dimensions, a star schema, or a bus matrix — declaring grain, choosing SCD types, identifying conformed dimensions and measures (additivity) — by grilling one step at a time. Also invoke for refining an existing DimML, or when the user says "ディメンショナル・モデリング", "ディメンションモデリング", "スタースキーマ", "バスマトリクス", "ファクト表を設計したい", "グレインを決めたい", "DimML を育てたい", "Kimball で整理したい".

Facilitate DDD domain modeling sessions via EventStorming conversation and DML (Domain Modeling Language). Use whenever the user wants to model a business domain by discovering domain events, commands, aggregates, policies, read models, and bounded contexts through dialogue. Produces incrementally-built DML as the primary artifact, plus a Markdown session report. Also invoke for refining existing DML, mapping out a new feature's domain model, or when the user says "ドメインモデリングしたい", "イベントストーミング", "DDDで整理したい", "DMLを育てたい".

review-all を実行し、指摘内容をコードに反映、bun run c / bun run lint / bun test で自己検証し、CONVERGED/NOT_CONVERGED の収束判定付き完了レポートを /tmp/arima-review-fix-result.md に出力する。レビュー→修正→検証→レポートを一気通貫で行うスキル。スコープ引数は /review-all と同じ（wt / PR #N / vs:<branch> / range / ファイル列挙）。review-fix-loop からの自動呼び出し（mode=non-interactive）にも対応。Use when user says 'レビューして直して', 'review and fix', '自動修正', 'レビュー反映', or when invoked by review-fix-loop.

Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Infer or annotate TCR antigen specificity by unsupervised clustering (TCRdist/tcrdist3, GLIPH2, clusTCR, GIANA) and database lookup (VDJdb, IEDB, McPAS-TCR), and rank candidates with supervised predictors (ERGO-II, NetTCR-2.x, pMTnet) under explicit caveats. Encodes the central truth that general TCR-epitope prediction for UNSEEN epitopes essentially does not work (collapses to near-random; IMMREP22, Grazioli 2022) because labeled data is dominated by a few immunodominant epitopes and there is no true negative set — so clustering for discovery is the honest task and de-novo binding needs wet-lab validation. Use when annotating TCR specificity or grouping a repertoire. Epitope/MHC context lives in mhc-binding-prediction.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across conditions.

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Controls error rates across thousands of simultaneous tests in genomics discovery using false-discovery-rate methods (Benjamini-Hochberg 1995; Benjamini-Yekutieli 2001 for arbitrary dependence; Storey q-value with pi0 estimation; local FDR; independent filtering Bourgon 2010; covariate-weighted FDR via IHW Ignatiadis 2016), plus family-wise error control (Bonferroni, Holm) and the GWAS genome-wide threshold. Covers the FDR-versus-FWER choice as the discovery-versus-confirmatory distinction, the dependence assumptions behind BH (PRDS) versus BY, pi0 estimation, the independent-filtering and false-coverage-rate traps, and reproducibility ranking via IDR (Li 2011). Use when correcting p-values from genome-wide tests, choosing between BH/BY/q-value/Bonferroni, setting an FDR threshold, applying IHW or independent filtering, or interpreting q-values. For confirmatory trials with few pre-specified endpoints (closed testing, graphical/gatekeeping), see clinical-biostatistics/multiplicity-graphical.

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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the p53-dependent G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Designs and analyzes pooled prime-editor (PE) screens for installing precise genetic variants without bystander confounding. Covers pegRNA design with PRIDICT and PRIDICT2 (Mathis 2023/2024) for predicting per-pegRNA editing efficiency, pegRNA architecture (spacer + scaffold + PBS + RTT), PE2 / PE3 / PE3b / PEmax / PEAR variants, MOSAIC in situ saturation mutagenesis (Hsu JY et al 2024 bioRxiv), the PRIME pooled-screen methodology (Erwood/Doman 2023 Nat Biotechnol 41:885; ~3,699 ClinVar variant screens), chromatin context as a primary determinant of PE efficiency, scaffold-incorporation and indel byproduct quantification with CRISPResso2, and the cross-modal validation strategy of PE + base-editor screens for variant function. Use when designing a pegRNA library for variant installation, choosing between BE and PE for a specific edit, predicting pegRNA efficiency before library synthesis, analyzing PE screen output, distinguishing intended-edit from scaffold-incorporation, or scaling PE screens to thousands of variants.

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Render the user's morning brief as a styled HTML artifact, or set it up as a recurring weekday task. Use only when the user explicitly asks to run, see, or set up their morning brief, or if they invoke /morning by name. A question about their day, schedule, or calendar is not by itself a request for the brief; answer it directly instead.

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Review a GitHub pull request from multiple perspectives in parallel, output only findings, then let the user pick which to fix in the same session. Use when the user asks to review a PR by number, mentions "PRレビュー" / "PR review" with a number, or invokes `/pr-review <number>`. Fans out subagents for absolute-rules, stop-slop, security, architecture, code-quality, testing, and ai-antipattern.

JSONで定義されたAPI仕様を元にRuby on RailsでAPIと管理画面を実装するスキル。全体のオーケストレーションを行い、各ステップの詳細ガイドラインに従って実装を進めます。

Hotwire（Turbo + Stimulus）を使用してRuby on Railsの管理画面を実装し、PlaywrightによるE2Eテストを含めた完全な実装を行うスキル

Sort AmeriFlux BASE-BADM BIF variables from Excel or CSV files into observation, management-event, static metadata, and plotting-ready target time-series tables. Use when Codex is asked to sort AmeriFlux BIF variables into time series; organize BADM/BIF variables by date; pivot AMF *_BIF_*.xlsx files by GROUP_ID; output total LAI, leaf mass per area, above-ground biomass, canopy height, fruit yield, or total yield time series; write MATLAB readers for BIF time-series plotting; or prepare dated AmeriFlux site observations and management records for EcoSIM workflows.

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Find nearby places (restaurants, cafes, bars, pharmacies, etc.) using OpenStreetMap. Works with coordinates, addresses, cities, zip codes, or Telegram location pins. No API keys needed.

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When the user wants to optimize content for AI search engines, get cited by LLMs, or appear in AI-generated answers. Also use when the user mentions 'AI SEO,' 'AEO,' 'GEO,' 'LLMO,' 'answer engine optimization,' 'generative engine optimization,' 'LLM optimization,' 'AI Overviews,' 'optimize for ChatGPT,' 'optimize for Perplexity,' 'AI citations,' 'AI visibility,' 'zero-click search,' 'how do I show up in AI answers,' 'LLM mentions,' or 'optimize for Claude/Gemini.' Use this whenever someone wants their content to be cited or surfaced by AI assistants and AI search engines. For traditional technical and on-page SEO audits, see seo-audit. For structured data implementation, see schema-markup.

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Restore working context saved earlier by /context-save. Loads the most recent saved state (across all branches by default) so you can pick up where you left off — even across Conductor workspace handoffs. Use when asked to "resume", "restore context", "where was I", or "pick up where I left off". Pair with /context-save. Formerly /checkpoint resume — renamed because Claude Code treats /checkpoint as a native rewind alias in current environments. (gstack)

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Build a "product description" repo for a software product — a set of prose documents describing, from the outside in, what the user sees, what they can do, and exactly what happens when they do it, written from the code and tests, then verified against the running product and triaged into a bug list. Works for any product with a user (canvas editors, web apps, CLIs, chat products, mobile apps). Use when the user asks to "write a product description for X", "describe the user experience of X", "document how X behaves for the user", "make a behavior-spec repo", or wants a feature-by-feature, event-by-event account of an app's behavior rather than API docs. Also use to resume or extend an existing product description repo.

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Run a fast, read-only health check across all skills in the library and produce a structured quality report — without modifying anything. Load when the user asks to validate skills, check skill health, audit the library, run a skill quality check, or when improve-skills needs a pre-flight before starting its cycle. Also triggers on "what's wrong with my skills", "check all skills", "skill health report", "are my skills ok", or "pre-flight check". Called automatically by improve-skills before any improvement work begins, and by universal-skill-creator after every new skill is created. Never modifies any file — only reads and reports.

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Detect and resolve naming collisions, overlapping intent triggers, and insufficient intent diversity across the skill library. Load when a new skill is created (called by universal-skill-creator), during improvement passes (called by improve-skills), or when the user asks to deconflict skills, check for naming collisions, audit trigger overlap, review intent coverage, find duplicate triggers, check skill names, or says "are any skills too similar", "which skills overlap", "deconflict the library", "check for confusing skill names", "intent audit".

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Internal skill. Called by setup-evaluation after a PASS. Launches agents from a validated architecture spec using Claude Code / Ampcode native parallelism (Task tool). Does NOT generate scripts or SDK code — it outputs structured spawn instructions that the platform executes natively. Never invoked directly by the user. Never launches without a setup-evaluation PASS.

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。