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概要と使いどころ
Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.
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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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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.
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Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.
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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.
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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Recommends RT-CGM devices for adult patients with well-controlled type 1 diabetes who are willing and able to use the devices on a nearly daily basis. Trigger phrases include 'Controlled T1DM patient interested in CGM' and 'Consider RT-CGM for glycemic stability in well-controlled T1DM'.
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If CGM fails or is removed, revert the insulin pump to manual mode provided basic criteria for pump use in hospital are still met. Trigger phrase: "CGM failed, should we switch pump to manual mode?
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Advises surgical referral for parathyroid carcinoma when feasible after achieving control of severe hypercalcemia. Triggered when a clinician confirms parathyroid carcinoma and inquires about curative options following medical stabilization of hypercalcemia.
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This skill provides a shared decision-making framework for selecting second-line therapies in patients with ACTH-dependent Cushing's syndrome who have persistent hypercortisolism after transsphenoidal surgery or for whom surgery is not feasible. Clinical triggers include "failed TSS", "non-curative pituitary surgery", "persistent UFC elevation post-op", and "surgery contraindicated".
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This skill recommends bilateral adrenalectomy for patients with Cushing's syndrome when bilateral adrenal pathology is confirmed as the source of hypercortisolism. Clinical triggers include bilateral macronodular adrenal hyperplasia (BMAH), bilateral adrenal adenomas, or bilateral adrenal carcinoma identified by imaging.
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This skill suggests pituitary-directed medical treatments (e.g., cabergoline, pasireotide) for patients with Cushing's disease who are not surgical candidates or have persistent disease after transsphenoidal surgery. Use when a CD patient cannot undergo surgery or has residual disease post-TSS; triggers include "not a surgical candidate", "persistent disease after TSS", "ongoing hypercortisolism despite prior surgery".
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Determines when adrenal venous sampling (AVS) is indicated for functional subtyping of primary aldosteronism (PA) when surgical treatment is feasible and desired by the patient. Triggered when a clinician confirms PA diagnosis and asks 'Do I need AVS for subtyping?' or evaluates surgical candidacy.
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Guides selection of the optimal confirmatory test (CCT, SIT, FUT, OSLT) for primary aldosteronism based on patient safety and feasibility. Triggers include when a clinician asks “Which confirmatory test should I use?” or evaluates patient comorbidities before testing.
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Determines whether to recommend unilateral laparoscopic adrenalectomy or medical therapy with a mineralocorticoid receptor antagonist for patients with confirmed unilateral PA (aldosterone-producing adenoma or unilateral adrenal hyperplasia). Triggered when discussing treatment options after confirming unilateral PA in a hypertensive patient with hypokalemia or resistant hypertension.
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Determines whether to perform adrenal venous sampling (AVS) to lateralize aldosterone excess in patients with confirmed primary aldosteronism (PA) who are being evaluated for surgical treatment. Indicated when surgery is feasible and desired by the patient, or when subtype workup is planned for a surgical candidate, especially in those younger than 35 years with spontaneous hypokalemia, marked aldosterone excess, and unilateral adrenal lesions on CT.
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Differentiates aldosterone-producing adenoma from idiopathic adrenal hyperplasia based on 18-hydroxycorticosterone levels, with APA patients generally having levels >100 ng/dL at 8:00 a.m. and IAH patients usually having levels <100 ng/dL. Use when reviewing 18-OHB test results to help subtype PA; triggers include 18-OHB >100 ng/dL (suggesting APA) or <100 ng/dL (suggesting IAH).
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Educates patients with primary adrenal insufficiency on increasing glucocorticoid dosage during intercurrent illness, fever (≥38°C), or physiological stress, including recognition of precipitating symptoms (e.g., fever, vomiting, trauma) and actions to prevent impending adrenal crisis. Trigger phrases: fever, intercurrent illness, stress, vomiting, inability to tolerate oral meds, need for parenteral glucocorticoid.
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Recommends increasing hydrocortisone dose in pregnant patients with primary adrenal insufficiency based on individual clinical course, especially during the third trimester. Trigger phrases include "fatigue, postural hypotension, weight loss, or hyperglycemia in pregnant PAI patient" and "need for glucocorticoid dose adjustment in third trimester."
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Helps distinguish unilateral from bilateral adrenal disease based on 18-oxocortisol levels, which are typically higher in aldosterone-producing adenoma than idiopathic adrenal hyperplasia. Use when evaluating 18-oxocortisol results during PA workup to guide subtype classification after a positive ARR.
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Suggests using morning cortisol ≤140 nmol/L (5 µg/dL) in combination with ACTH as a preliminary test suggestive of primary adrenal insufficiency when a corticotropin stimulation test is not feasible. Use when patients present with indicative symptoms such as hypotension, hyponatremia, hyperkalemia, or fatigue and corticotropin stimulation testing cannot be performed.
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In patients with adrenal insufficiency receiving dexamethasone replacement, the guideline suggests increasing the dexamethasone dose when enzyme-inducing antiepileptic drugs are co-administered. Trigger phrases include "AI patient on dexamethasone starts enzyme-inducing antiepileptic drug" or "AI patient on dexamethasone requiring enzyme-inducing AED".
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In central hypothyroidism patients receiving levothyroxine who initiate enzyme‑inducing antiepileptic drugs, the guideline recommends checking free T4 at least 6 weeks after AED start and increasing the levothyroxine dose if free T4 falls below the target range. Triggers include: central hypothyroidism patient on levothyroxine starting antiepileptic drug such as phenytoin, carbamazepine, or oxcarbazepine.
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Draft or revise English prose for any brief — documentation body, intake problem statements, spec context, RCA summaries, marketing copy, README sections, PR descriptions. Mandatorily invokes `Skill(humanizer)` as the final pass on every draft. Conditionally invokes `copywriting` for persuasive register, `documentation` for reference docs, `technical-tutorials` for tutorials. Used when any phase needs human-readable prose written or rewritten. Composition only — research and register-picking happen in the caller's context.
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。