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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Solve ordinary differential equations (initial and boundary value problems). Supports stiff/non-stiff systems, event detection, Hamiltonian/symplectic integration, parameter sweeps, and phase space analysis. Use for any ODE system in physics, engineering, or applied math.

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Computational fluid dynamics — Navier-Stokes solvers, lid-driven cavity, channel flow, vortex methods, turbulence statistics, drag/lift computation. Spectral and finite-difference methods for incompressible and compressible flows.

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Generate the success criteria for a task or question, then review work against them. Given a task, goal, or open-ended question, decompose it into scenarios, evaluation perspectives, and fine-grained weighted YES/NO criteria using the Recursive Expansion Tree (RET) method; if work is supplied, score it criterion-by-criterion and surface what is missing or could be better. Use when asked to self-review or check your own work, judge whether a task is done well or completely, build a definition-of-done or completeness checklist, create an evaluation rubric or grading criteria, score or grade answers to a question, set up an LLM-as-judge rubric, or when the user mentions self-review, completeness check, success criteria, evaluation criteria, scoring rubric, Qworld, or the RET algorithm.

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Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki). Fits the MM equation by nonlinear regression (and reports Lineweaver-Burk for reference). Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor. NOT for BRENDA database lookups of published constants (use the BRENDA tools).

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Drug and chemical toxicity assessment via adverse outcome pathways (AOPs), real-world FAERS adverse event signals, FDA labels, and toxicogenomic associations. Triangulates molecular initiating event to cellular outcome to organ-level toxicity to clinical adverse event. Use for hepatotoxicity/cardiotoxicity/nephrotoxicity prediction and toxicology reports.

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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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任意の対象リポジトリに Claude Code の .claude/ 体系（CLAUDE.md・Agents・Rules・Skills・hooks）を 初期セットアップする。「claude セットアップして」「.claude 作って」「CLAUDE.md 初期化」「Agent 整備して」 「claude-code セットアップ」などで使用。既存 .claude/ の差分充実は update-claude を使用。 implement-issue-tree が動く前提（gh auth / sub_issues / workflow js）の整備まで含む。

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GitHub Project v2 を新規作成し、Status/Priority/Size の標準フィールドを設定してリポジトリにリンクする。Auto-add/Auto-archive/Auto-close 等のビルトインワークフロー設定 URL もガイド (CLI 不可・Web UI のみ)。「プロジェクト作って」「Project v2 セットアップ」「カンバン作成」などで使用。

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Theatre.js アニメーションツールキットリファレンス。 @theatre/core / @theatre/studio / @theatre/r3f / @theatre/dataverse。 getProject, Sheet, Sequence, Object, val, onChange, prop-types（number / rgba / compound / image）。 studio initialize / extend / transaction / scrub / createPane。 SheetProvider, editable, useCurrentSheet, useVal, usePrism, useAtom。 keyframe アニメーション、audio sync、state JSON、React Three Fiber 統合。

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TanStack Virtual (React 仮想スクロール、@tanstack/react-virtual) の API リファレンス。 useVirtualizer, useWindowVirtualizer, Virtualizer, VirtualItem, estimateSize, measureElement, rangeExtractor, overscan, lanes, getVirtualItems, getTotalSize, scrollToIndex。固定/可変/動的計測、grid、sticky header、infinite scroll、table、 window scroll 仮想化。別名 react-virtual, virtual-core。 react-flow / Compose LazyColumn / WinUI ListView とは別（DOM 向けヘッドレス仮想化）。

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TanStack Query (React Query) v5 (@tanstack/react-query) の API リファレンス。 useQuery, useQueries, useInfiniteQuery, useMutation, useSuspenseQuery, QueryClient, QueryClientProvider, queryOptions, HydrationBoundary, invalidateQueries, prefetchQuery, skipToken, keepPreviousData, placeholderData, staleTime, gcTime, optimistic updates, SSR / hydration, persistQueryClient, eslint-plugin-query。 kubb（フック生成側）とは別。

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Claude API (platform.claude.com) の tool use / Agent Skills / MCP。 tool definition (JSON Schema), tool_use / tool_result, server tools（code execution, web search, web fetch, memory tool, tool search）, client toolset（computer use, browser use）, Agent Skills (SKILL.md), Skills API GA (/v1/skills), MCP connector, mcp_servers, mcp_tool_listing, MCP tunnels, Tunnels API。

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NVIDIA DGX Spark User Guide リファレンス。GB10 Grace Blackwell Superchip 仕様、 first-boot / UEFI、ConnectX-7 Networking (旧 Spark Stacking)、複数 Spark 接続、 NVIDIA Sync Cluster Assistant、DGX OS / NGC / container runtime、 Release Notes (DGX OS 7.5.0)、known issues、PXE / cloud-init、fleet 運用、 apt / fwupdmgr、recovery、PSIRT、 NVIDIA Developer Forums 由来 troubleshooting、 build.nvidia.com/spark playbook (vLLM / vLLM cluster / TensorRT-LLM / Ollama / ComfyUI / NIM / NeMo / VLM fine-tuning / NVIDIA PAIR / NCCL)、Tailscale、VS Code。

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Manages shadcn components and projects — adding, searching, fixing, debugging, styling, and composing UI, including chat interfaces. Provides project context, component docs, and usage examples. Applies when working with shadcn/ui, component registries, presets, --preset codes, or any project with a components.json file. Also triggers for "shadcn init", "create an app with --preset", "switch to --preset", and for building a design system or applying a DESIGN.md or brand spec to shadcn/ui.

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Identify the first beachhead market segment for a product launch. Evaluates segments against burning pain, willingness to pay, winnable market share, and referral potential. Use when choosing a first market, targeting an initial customer segment, or planning market entry strategy.

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Predicts protein-coding gene structures (exons, introns, UTRs) in eukaryotic genomes with BRAKER3 (RNA-seq + protein evidence), BRAKER1/BRAKER2, GALBA (protein-only), Funannotate (fungi), GeMoMa (homology projection), or Helixer/Tiberius (deep-learning ab initio). Covers the evidence-first tool decision, mandatory soft-masking, the training-set-quality-dominates principle, OrthoDB clade-partition selection, the one-isoform-per-locus and missing-UTR traps, merge/split errors, and reference bias against orphan genes. Use when annotating a newly assembled eukaryotic genome, choosing a gene-prediction pipeline based on available evidence, or diagnosing a poor annotation.

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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.

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Infers person-to-person transmission from pathogen genomes using outbreaker2 (Campbell 2018), TransPhylo (Didelot 2017), phybreak (Klinkenberg 2017), BadTrIP (De Maio 2018), SCOTTI (De Maio 2016), BEASTLIER (Hall 2015), and SNP-distance / cluster-picker approaches (HIV-TRACE for HIV; transcluster). Defines outbreak clusters using pathogen-specific SNP thresholds (NOT a universal cutoff -- TB <=12 SNPs / Walker 2013; MRSA <=15 / Coll 2017; C. difficile <=2 / Eyre 2013; Klebsiella <=21 / Snitkin 2012), models within-host diversity and transmission bottlenecks (Worby-Lipsitch-Hanage 2014; McCrone 2018; Sobel Leonard 2017; Lythgoe 2021 SARS-CoV-2), integrates contact-tracing data, distinguishes generation interval from serial interval (Britton & Scalia Tomba 2019; Ali 2020), attributes source via Bayesian source attribution (Mather 2013 DT104; islandR), and reconciles transmission-network reconstruction with epi metadata. Use when investigating outbreaks for who-infected-whom, defining SNP-cluster outbreak definitions, accounting for unsampled intermediates, choosing between outbreaker2 (rich epi data) and TransPhylo (genomic-only after dated phylogeny), running source attribution between host populations, calling HIV-TRACE thresholds appropriate to the local subtype, or distinguishing recent transmission from reactivation in TB / chronic HIV.

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Assigns isolate identity at the right resolution for the question -- ANI / Mash species triage, 7-locus MLST historical comparability, cgMLST / wgMLST outbreak resolution (chewBBACA, BIGSdb, Ridom SeqSphere, EnteroBase HierCC), in-silico serotyping (SISTR, SeqSero2 for Salmonella; SerotypeFinder for E. coli; Kaptive K/O for Klebsiella; SeroBA for pneumococcus; spa + SCCmec for S. aureus), and lineage callers (TB-Profiler / Mykrobe Coll-Napier barcode for MTBC, Pangolin + Nextclade for SARS-CoV-2, PopPUNK GPSC for S. pneumoniae). Use when typing bacterial isolates for surveillance or outbreak investigation, choosing between cgMLST allele distance and core-SNP distance for cluster definition, harmonising calls across schemas / database versions (chewBBACA vs Ridom vs EnteroBase), assigning MTBC lineage with the Napier 2020 90-SNP barcode, calling Salmonella serovar via SISTR with monophasic Typhimurium awareness, running Pangolin UShER mode with explicit pangolin-data version pinning, or selecting a typing resolution to match the surveillance question.

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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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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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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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