「pair」の検索結果

Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.

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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.

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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Calls microsatellite instability from WES/WGS/targeted-panel with MSIsensor, MSIsensor-pro, MSIsensor-ct (panel-aware), mSINGS, and MANTIS for FDA pembrolizumab MSI-H pan-tumor / Lynch syndrome / dMMR ICI biomarker. Use when stratifying ICI eligibility (Le 2015), pairing MSI with TMB-H (Sha 2020 / Salem 2018), screening Lynch syndrome (universal IHC + MSI), or distinguishing MSI-H tumors from POLE-exo hypermutator with overlapping signatures.

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Tests associations between categorical variables in clinical data using chi-square, Fisher's exact, Boschloo, Cochran-Mantel-Haenszel, and modern McNemar variants with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen). Use when analyzing categorical outcomes, paired binary endpoints, or testing treatment-outcome independence in confirmatory or exploratory clinical trials.

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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Suggests real-time CGM over no CGM for outpatients with type 2 diabetes who use insulin and/or sulfonylureas and are at high risk for hypoglycemia to detect and prevent low glucose events. Consider when initiating CGM in T2D patients on insulin/SU with a history of severe hypoglycemia or impaired awareness of hypoglycemia (IAH).

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This skill determines whether an adolescent or adult patient meets DSM-5 criteria for gender dysphoria (gender incongruence) by evaluating the presence of at least two of six specified criteria over a minimum 6-month duration, accompanied by clinically significant distress or impairment. It is triggered when a clinician queries whether the patient's reported symptoms align with gender dysphoria, such as persistent incongruence between experienced/expressed gender and designated gender.

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Assess whether a hospitalized adult with diabetes on insulin pump therapy remains a candidate for continued inpatient pump use. Consider triggers such as the clinician asking "Is this patient appropriate to continue insulin pump in hospital?" and evaluate for impaired consciousness, inability to adjust pump settings, critical illness, DKA, or hyperosmolar hyperglycemic state.

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Adjusts intravenous bisphosphonate dosing and infusion duration for patients with hypercalcemia of malignancy and renal insufficiency (creatinine clearance <60 mL/min). Triggered when a clinician encounters renal impairment and asks how to modify zoledronic acid or pamidronate infusion rates.

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Complete bedside prescribing reference for Mirago (mirabegron, beta-3 adrenoceptor agonist) for overactive bladder — covering contraindications, safety screening, drug interactions, dose selection in special populations, titration, and administration. Use when a clinician asks how to start mirabegron, what dose to use in renal or hepatic impairment, is mirabegron safe in this patient, mirabegron drug interactions, or Mirago for OAB.

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Report the health of the central system spec at `docs/system/` across seven checks — coverage gaps, stale elements, dangling anchors, duplicate anchors, orphan shards, unillustrated elements, and shards missing their kind annotation. Report-first and read-only: it repairs nothing until a human confirms a specific item. Use when the corpus has drifted, after a merge that touched `docs/system/`, or from `/archive` Step 5.5 in report-only mode. Requires `memory.architecture_map.enabled`.

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Decompose an approved spec into a dependency-ordered swarm plan — one task per component, each with an explicit write_set. Produces `.claude/state/swarm/<slug>.json` with tasks + waves. The wave scheduler guarantees pairwise-disjoint write_sets within each wave so parallel dispatch is provably conflict-free.

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Split a dirty working tree into single-concern Conventional Commits. The deterministic inventory.mjs helper groups dirty paths by concern (docs, source + paired test, config, governance); main context refines the grouping and presents a commit plan. Read-only until the user approves the plan — it never stages, never commits, never touches consent paths. Disjoint from the commit skill (Phase 11 executor): the planner proposes a split; the executor lands one consented commit. Use when a working tree has accumulated heterogeneous changes that should not land as one commit.

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Cycle-end retrospective converting recurring judgment failures into durable enforcement. Reviews the cycle's friction — repeated user corrections, guard trips, RCA themes, integrate failures — and turns each recurring one into a landmines.md entry, then proposes graduation candidates up the enforcement funnel (landmine → advisory hook → hard gate). Pairs with standup: standup says what shipped and what's next; retrospective says what kept going wrong and how to stop it structurally. Writes only memory entries and a report — graduation proposals are advisory and require the normal seed.md amendment path to become enforcement. Invoke at the end of a release cycle, an epic, or any stretch of work with repeated friction.

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Generate or repair a project's .gitignore. Composes the baseline must-ignore set (the single source of truth in baseline-ignores.json) with optional gitignore.io enrichment, and merges add-only so existing entries are never lost. Use when a repo has no .gitignore, when the commit-leak guard reports a gap, or when onboarding a new stack. Trigger: "set up gitignore", "fix my gitignore", "ignore node_modules/secrets", "gitignore for <stack>".

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This skill should be used when the user asks to "implement LLM-as-judge", "compare model outputs", "create evaluation rubrics", "mitigate evaluation bias", or mentions direct scoring, pairwise comparison, position bias, evaluation pipelines, or automated quality assessment.

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Clone or recreate a live website URL, page, or section as React + Tailwind with extracted DOM, CSS, assets, responsive layout, motion, and interactions. Use for live-URL implementation or fidelity repair; not capture-only or diff-only requests.

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Diagnose why an existing implementation differs from reference evidence using AE/SSIM, pixel, section, computed-style, and transition diffs. Use for post-implementation mismatch or repair guidance; not baseline capture or full clone generation.

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Add a new E2E test case to tests/e2e/prompts.yaml for LangSmith evaluation. Use when adding interaction pairs to test, covering new ANSM drug classes, or rebalancing eval coverage.

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