「method」の検索結果

Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and posterior probability stopping rules. Covers FDA Bayesian Devices Guidance (2010), FDA Bayesian Methodology in Drugs Draft (January 2026), BOIN Fit-for-Purpose qualification (December 2021), and Project Optimus dose-optimisation. Use when designing dose-finding studies, platform trials, or sensitivity analyses with informative priors.

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Parameter-efficient fine-tuning for LLMs using LoRA, QLoRA, and 25+ methods. Use when fine-tuning large models (7B-70B) with limited GPU memory, when you need to train <1% of parameters with minimal accuracy loss, or for multi-adapter serving. HuggingFace's official library integrated with transformers ecosystem.

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Discover conserved quantities and symmetries from trajectory data. Identifies energy, momentum, angular momentum, and custom invariants using neural networks and symbolic methods. Inspired by Noether's theorem.

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Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.

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Reduce LLM size and accelerate inference using pruning techniques like Wanda and SparseGPT. Use when compressing models without retraining, achieving 50% sparsity with minimal accuracy loss, or enabling faster inference on hardware accelerators. Covers unstructured pruning, structured pruning, N:M sparsity, magnitude pruning, and one-shot methods.

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Explains ML predictions on omics data with SHAP, LIME, and permutation importance, handling the correlated-feature trap, the conditional-vs-interventional Shapley choice, and the attribution-is-not-causation boundary. Use when interpreting an omics classifier, debugging shortcut/batch learning, or deciding whether an attribution ranking can be trusted as biology. For validated feature selection see machine-learning/biomarker-discovery; explanations are not a selection method.

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Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with explicit out-of-distribution and label-transfer uncertainty. Use when annotating new single-cell datasets against a pre-trained reference, deciding which mapping method fits, or judging whether transferred labels are trustworthy. For de novo clustering and manual annotation see single-cell/cell-annotation; for batch integration without a reference see single-cell/batch-integration.

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ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.

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End-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition with MANDATORY PERMANOVA + PERMDISP pair (Anderson & Walsh 2013), constrained ordination, and the read-counts-not-abundance critique (Lamb 2019). Use when processing eDNA samples for biodiversity assessment, deciding ASV vs OTU, configuring OBITools3 v3, interpreting decontam screening, or reporting community comparisons with the dispersion confound check.

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End-to-end clinical trial analysis workflow from CDISC SDTM/ADaM loading through ICH E9(R1) estimand-driven primary analysis to CONSORT 2025 regulatory-compliant reporting. Covers data preparation, FDA 2023 marginal vs conditional logistic regression, categorical tests with Boschloo, modern HTE/subgroup methods, missing-data sensitivity (MMRM, reference-based MI, Permutt tipping point), graphical multiplicity (Bretz-Maurer), survival analysis (Cox/RMST/competing risks) when applicable, and Table 1. Use when performing a complete analysis of clinical trial data.

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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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Authors reproducible bioinformatics pipelines with Snakemake - rules wired by output-file pattern, wildcards and expand() for sample fan-out, checkpoints for runtime-unknown outputs, resource/retry escalation, and conda/container software deployment on HPC and cloud. Use when deciding rule-based (Snakemake) vs channel/dataflow (Nextflow) authoring; wiring rules by OUTPUT-file pattern rather than imperative order; using wildcards + expand() for sample fan-out and constraining them to stop silent mis-routing; adding checkpoints when the set of outputs is unknown until a step runs (dynamic DAG); diagnosing why a job reran (or did not) under the mtime-plus-provenance trigger set; escalating memory on retry for OOM-killed jobs; and porting a Snakemake 7 `--cluster`/remote-provider command to the Snakemake 8+ executor-plugin and storage-plugin model (snakemake-executor-plugin-slurm) with `--software-deployment-method`.

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Authors portable, strongly-typed bioinformatics pipelines in the Common Workflow Language (CWL v1.2) as CommandLineTool/Workflow/ExpressionTool documents, validated with cwltool and run at scale on Toil/Arvados/Calrissian. Use when deciding CWL (portability/provenance/regulated) vs Nextflow/WDL/Snakemake; declaring secondaryFiles for indexed companions (.bai/.fai/.dict/.tbi and the caret rule); putting resources/containers under requirements (must-hold) vs hints (advisory) to avoid silent OOM; choosing scatterMethod (dotproduct vs flat_/nested_crossproduct); preferring $(...) parameter refs over ${...} JavaScript for portability; pinning DockerRequirement images; or emitting a CWLProv provenance object for audited/clinical settings.

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End-to-end post-GWAS causal inference pipeline orchestrating heritability partitioning, genetic correlation, Mendelian randomization with CHP-aware sensitivity (CAUSE / LHC-MR), colocalization, fine-mapping with SuSiE / FOCUS, mediation, TWAS triangulation, cis-pQTL drug-target MR, effector-gene prioritization (L2G / PoPS / cS2G), and GenomicSEM common-factor GWAS. Use when triangulating causal inference across multiple complementary methods, prioritizing tissues via stratified LDSC, nominating or de-risking drug targets, mapping a lead SNP to a candidate effector gene, modeling shared genetic architecture across correlated traits, or producing a STROBE-MR-compliant publication-grade evidence battery from GWAS summary statistics.

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TOP PRIORITY skill — find and immediately fix or remove every piece of wrong, outdated, or redundant information in ToolUniverse docs. Wrong code, broken links, incorrect counts, and overlapping instructions must be fixed or removed — never left in place. Runs five phases: (D) static method scan, (C) live code execution, (A) automated validation, (B) ToolUniverse audit, (E) less-is-more simplification. Core philosophy: each concept appears exactly once; remove don't add; no emojis; single setup entry point. Use when reviewing docs, before releases, after API changes, or when asked to audit, fix, or simplify documentation.

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Create high-quality ToolUniverse skills following test-driven, implementation-agnostic methodology.

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Multi-method binding pocket detection and druggability assessment. Grid-based, fpocket, and P2Rank detection with druggability scoring, visualization, and cross-structure comparison.

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Hybrid ML + physics binding affinity prediction. Empirical scoring, MM/GBSA rescoring, multi-method consensus, and batch virtual screening for protein-ligand complexes.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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Designs and validates quantitative targeted metabolomics assays (MRM/SRM on triple-quadrupole, PRM on high-resolution instruments) to report absolute concentrations. Covers the internal-standard strategy (external cal -> global IS -> standard addition -> stable-isotope-labeled IS), weighted calibration judged by back-calculated %RE not R-squared, ion-ratio quantifier/qualifier confirmation, matrix-effect/recovery characterization, and ICH M10 method validation. Use when quantifying a closed panel of known metabolites with units, building or validating an LC-MS/MS assay, choosing an IS or calibration weighting, or judging whether a reported concentration is trustworthy. For untargeted feature detection see metabolomics/xcms-preprocessing; for group statistics see metabolomics/statistical-analysis; for flux/MID/tracing see metabolomics/isotope-tracing.

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Designs QC, corrects signal drift, removes batch effects, filters features, normalizes samples, and imputes missing values for untargeted LC-MS/GC-MS metabolomics, framing each step as a measurement model that can create or erase biological signal. Use when processing a peak/feature table before statistical analysis, choosing a drift-correction or sample-normalization method, deciding QC RSD vs D-ratio filtering, or handling left-censored missing values. The feature table is produced by metabolomics/xcms-preprocessing or metabolomics/msdial-preprocessing; transformation/scaling for modeling defers to metabolomics/statistical-analysis; cross-study design issues link to experimental-design/batch-design.

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Facilitate interactive brainstorming sessions using diverse creative techniques and ideation methods. Use when the user says help me brainstorm or help me ideate.

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Walk every branching path and boundary condition in content, report only unhandled edge cases. Orthogonal to adversarial review - method-driven not attitude-driven. Use when you need exhaustive edge-case analysis of code, specs, or diffs.

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