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概要と使いどころ
Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.
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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.
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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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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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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.
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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.
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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.
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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.
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Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.
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Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.
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This skill determines whether inpatient diabetic patients meet high-risk criteria for CGM initiation using Table 3 factors such as age ≥65 years, BMI ≤27 kg/m², type 1 diabetes, insulin regimen, and specific clinical conditions. It is triggered by clinician questions like "Should I assess this inpatient for CGM initiation based on hypoglycemia risk?" or "Is this patient a candidate for inpatient CGM?"
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Suggests initiating inpatient continuous glucose monitoring (CGM) for select hospitalized patients at high risk for hypoglycemia, combined with periodic point-of-care glucose checks for accuracy. Triggers include planning glucose monitoring for inpatients with prior severe hypoglycemia, renal or hepatic dysfunction, or age 65 years or older.
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Recommends initial surgical resection of the primary lesion(s) causing Cushing's syndrome when surgery is feasible and likely to significantly reduce glucocorticoid excess. Trigger phrases include overt Cushing's syndrome, ACTH-dependent CS, ectopic ACTH secretion, adrenal adenoma, bilateral macronodular adrenal hyperplasia, and persistent hypercortisolism.
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This skill provides structured education to patients and families about Cushing's syndrome pathophysiology, treatment options, and post-remission expectations. It is triggered when a clinician encounters a new Cushing's syndrome patient or family needing disease information, such as at initial diagnosis or before treatment initiation.
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Recommends initiating intravenous isotonic saline hydration as initial management for hypercalcemia of malignancy (HCM) while awaiting antiresorptive therapy, with fluid rate adjusted according to cardiac function. Triggered when a clinician encounters a patient with HCM (e.g., serum calcium >12 mg/dL, symptoms of hypercalcemia) and seeks immediate measures before specific drugs are available.
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Recommends withdrawing interfering medications and repeating aldosterone-to-renin ratio screening when initial screen is negative but clinical suspicion remains due to hypokalemia or medication interference. Trigger phrases include "initial screen negative", "hypokalemia", "resistant hypertension", and use of MRAs, ACE inhibitors, ARBs, beta-blockers, clonidine, or alpha-methyldopa.
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Azure Identity SDK for .NET. Authentication library for Azure SDK clients using Microsoft Entra ID. Use for DefaultAzureCredential, managed identity, service principals, and developer credentials.
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Automate AWS secrets rotation for RDS, API keys, and credentials
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Expert-level statics covering equilibrium of rigid bodies, free body diagrams, trusses, frames, friction, centroids, and moments of inertia.
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Expert-level calculus knowledge. Use when working with limits, derivatives, integrals, multivariable calculus, vector calculus, differential equations, series, or optimization. Also use when the user mentions 'derivative', 'integral', 'limit', 'chain rule', 'gradient', 'divergence', 'curl', 'Taylor series', 'Fourier series', 'partial derivative', 'double integral', 'line integral', 'Stokes theorem', or 'Lagrange multipliers'.
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Turn a wireframe and everything already agreed into a written spec in traditional agile shape — an initiative broken into epics, epics into user stories with acceptance criteria, and themes as the labels that span them — presented as an interactive drill-down tree the user prunes, edits and annotates in the browser, with a plain-markdown spec generated from it. Use when the user wants a spec, an initiative or epic broken into user stories, acceptance criteria, to formalise what a wireframe or mockup does, or to review and edit a spec visually.
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Normative sufficiency conditions for Initial Boundary Conditions (IBCs) and the SOP for the cheap-tier boundary refinement loop (/boundary). Trigger when: - Crafting, auditing, or refining a prompt/IBC destined for an expensive (architect-class) model or an autonomous worker dispatch. - Evaluating whether a task frame is sufficient to bound an agent walk. - Prompt contains: /boundary, IBC, initial boundary condition, boundary contract, sufficiency conditions, worker prompt, prompt refinement.
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Remove AI-generated writing patterns from Egyptian Arabic (عامية مصرية / Masri) text. Use when editing or reviewing Egyptian dialect text to make it sound authentically human-written.
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Use this skill for any website, web application, frontend UI, component, layout, styling, refactor, or review. It enforces a self-contained editorial output standard: image-first composition, oversized typography, visible hairline grids, hard-edged rectangular framing, restrained copy, and review.
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