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概要と使いどころ
Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).
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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 7.
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Build interactive HTML/web visualizations with plotly (Python/R), bokeh (Python), and gganimate/plotly frames for animation, with awareness of current Kaleido static-export model (post-orca-EOL), HTML file-size bloat, and the limits of interactive-only output for journal submission. Use when producing zoomable/hoverable plots for notebook EDA, supplementary HTML, dashboards, or animated time-course / iteration visualizations.
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Sparse Identification of Nonlinear Dynamics (SINDy) — discover governing equations from time-series data. Builds sparse dynamical system models dx/dt = f(x) from measurements using PySINDy. Use when you have trajectory data and want to find the underlying ODE.
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Train Physics-Informed Neural Networks (PINNs) using DeepXDE. Solve forward and inverse PDE problems by embedding physics equations into the neural network loss function. Supports 1D/2D/3D, time-dependent, and parametric PDEs.
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Cost modeling and ROI analysis for specialized LLM development. Use when deciding whether to train a custom model, estimating total cost, or calculating break-even vs frontier APIs. Covers training costs, inference costs, and time-to-ROI projections.
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Training patterns for autoregressive neural PDE solvers (FNO, DeepONet, CNO). Covers rollout training, noise injection for stability, multi-component loss functions (H1, frequency-sensitive, boundary-aware), per-channel normalization for coupled multi-variable systems, and the PDEBench nRMSE metric. Use when training any neural operator that predicts time-dependent PDE solutions.
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RNN+Transformer hybrid with O(n) inference. Linear time, infinite context, no KV cache. Train like GPT (parallel), infer like RNN (sequential). Linux Foundation AI project. Production at Windows, Office, NeMo. RWKV-7 (March 2025). Models up to 14B parameters.
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Hamiltonian mechanics — symplectic integrators (leapfrog, Yoshida), Hamilton's equations, Poisson brackets, canonical transformations, action-angle variables, and KAM theory analysis. Use for energy-conserving long-time integration of conservative systems.
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Open-source AI observability platform for LLM tracing, evaluation, and monitoring. Use when debugging LLM applications with detailed traces, running evaluations on datasets, or monitoring production AI systems with real-time insights.
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Builds diagnostic and prognostic classifiers on omics feature matrices with regularized logistic regression, random forest, and gradient-boosted trees, handling the p>>n regime, batch shortcut learning, class imbalance, and probability calibration. Use when building a classifier from expression, methylation, or variant data, choosing an algorithm for high-dimensional small-n data, or diagnosing a suspiciously perfect AUC. For unbiased evaluation see machine-learning/model-validation; for feature selection see machine-learning/biomarker-discovery; for time-to-event outcomes see machine-learning/survival-analysis.
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Install the ToolUniverse Claude Code plugin in one step — provides MCP server with 1000+ scientific tools, 120+ research skills, slash commands, hooks, and the research agent. Use for first-time plugin install, troubleshooting plugin not loading, verifying MCP server connection, listing API key requirements, or configuring auto-update.
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Install or update ToolUniverse in Claude Science — create the conda env, install the tooluniverse pip package, and (re)build the tooluniverse-research skill by fetching the current workflow library from GitHub. Use for first-time setup, upgrading the ToolUniverse version, refreshing the bundled workflows after an upstream release, or reinstalling on a new machine.
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Authors reproducible Nextflow DSL2 pipelines built on reactive dataflow, where processes communicate only through channels and execution order is not guaranteed. Use when deciding channel/dataflow (Nextflow) vs rule-based (Snakemake) authoring; wiring queue vs value channels and fixing shared-reference exhaustion with .first(); composing DSL2 modules and subworkflows with take/main/emit; selecting container/conda profiles and pinning images by digest for portability across local/SLURM/LSF/AWS Batch/Google Batch/Kubernetes executors; diagnosing why -resume misses the cache (nondeterministic input order, mtime on network filesystems, mutable :latest tags) with cache 'lenient' and -dump-hashes; managing work/ vs publishDir and dynamic retry escalation; and choosing whether to adopt an nf-core community pipeline or author from scratch.
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Programmatic untargeted LC-MS feature extraction in R with the modern xcms 4.x MsExperiment/XcmsExperiment API, taking raw mzML to a feature table via CentWave peak detection, retention-time alignment, peak-density correspondence, gap-filling, CAMERA redundancy collapse, and built-in QC feature filtering. Use when converting centroided LC-MS runs into a features-by-samples matrix and deciding centWave/grouping/alignment parameters. For drift correction and QC/CV filtering execution see metabolomics/normalization-qc; for metabolite identification see metabolomics/metabolite-annotation; for the MS-DIAL GUI alternative with MS2Dec deconvolution see metabolomics/msdial-preprocessing; for downstream statistics see metabolomics/statistical-analysis.
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Use every time you push a commit to an active pull request, to verify the PR is truly stable before reporting merge readiness. Covers the post-push wait window, AI review audit (Copilot/Greptile/Codex), and the gh commands to snapshot PR state. Trigger on "I pushed" or "is the PR ready to merge".
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Progressively activates todo tests one at a time, updates implementation code until each passes (verified via Wallaby), checks off matching design doc progress, then moves to the next—following the design doc as the single source of truth.
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Implement damage, healing, status effects, alerts, movement modifiers, and timed gameplay effects consistently.
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Maintain English-source localization, adding Russian only when requested, with correct owner paths, variables, selectors, and runtime behavior.
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Integrate HTTP APIs, webhooks, external processes, retries, timeouts, caching, and secret-backed configuration safely.
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When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value. Also use when the user mentions "onboarding flow," "activation rate," "user activation," "first-run experience," "empty states," "onboarding checklist," "aha moment," or "new user experience." For signup/registration optimization, see signup-flow-cro. For ongoing email sequences, see email-sequence.
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Build AI time series forecasting systems. TRIGGERS - Use when user needs help with ai-forecasting-system related tasks.
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Resize a product photo to Shopify's recommended 2048×2048px square format, sharpen, and convert to WebP for fast storefront load times.
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Extract proof-of-delivery number, recipient, delivery time, items, exceptions, and signature status from delivery receipts.
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