「edge」の検索結果

Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Infer gene regulatory networks from bulk or general expression data with mutual-information (ARACNe) and tree-ensemble (GENIE3, GRNBoost2) methods, and infer transcription-factor protein activity from regulons with VIPER and msVIPER. Covers the activity-not-edges paradigm, the undirected-association caveat, the DREAM5 wisdom-of-crowds and method-complementarity result, AUPRC-over-AUROC evaluation, and gold-standard incompleteness. Use when inferring a regulatory network from a bulk expression matrix, finding master regulators, or scoring TF activity from a signature. For single-cell motif-pruned regulons see scenic-regulons; for co-expression modules see coexpression-networks.

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Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample distance heatmaps, top-DE-gene heatmaps with the row-scaling trap, dispersion / BCV plot interpretation, p-value histogram diagnostics, plotCounts for individual genes, blind=TRUE vs FALSE rationale, and the n=3 visualization stake. Use when generating DE diagnostic plots, choosing VST vs rlog for visualization, troubleshooting suspicious plot patterns (shifted MA cloud, batch-dominated PCA, anti-conservative p-value histogram), or building a standard QC figure panel.

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Visualize biological networks (PPI, gene-regulatory, co-expression, pathway) with layout algorithm choice (ForceAtlas2, Fruchterman-Reingold, Kamada-Kawai, hive plots), edge bundling, community-based coloring, and reproducible seeds using NetworkX, PyVis, igraph, and Cytoscape automation. Use when rendering biological networks for static publication, interactive HTML exploration, or Cytoscape-format export.

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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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Analyzes CRISPR drug-modifier (chemogenomic) screens with drugZ (Colic et al. 2019 Genome Med), a bidirectional Z-score method that identifies synthetic-lethal sensitizing genes and resistance-conferring suppressor genes from vehicle vs drug comparisons. Covers vehicle-anchored design (not Day-0), the bidirectional Z math giving greater sensitivity to small-effect hits than MAGeCK / STARS / edgeR / RIGER on drug screens, per-gene sumZ and normZ, synth (sensitizer) vs supp (suppressor) FDR, multi-dose handling, integration with control sgRNAs, and comparison with MAGeCK MLE with dose covariate. Use when running a drug-modifier CRISPR screen, identifying sensitizing or resistance genes for a drug candidate, choosing drugZ vs MAGeCK MLE for chemogenomic analysis, troubleshooting low-effect drug screens where MAGeCK lacks sensitivity, or designing a drug-screen layout (vehicle vs drug arms).

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Detect, date, and contextualize whole-genome duplication (WGD / paleopolyploidy) events using wgd v2 (Chen et al 2024), KsRates (Sensalari 2022 substitution-rate-corrected Ks dating), DupGen_finder (Qiao 2019), MAPS (Li 2018 phylogenomic), POInT (Conant 2008 ordered-block), SLEDGe (2024 ML-based), Whale.jl (Bayesian DL+WGD), and synteny-anchored paranome construction. Use when identifying ancient polyploidy from Ks distributions and synteny block analysis, positioning WGD events relative to speciation, distinguishing tandem from segmental from WGD duplications, dating the 2R/3R vertebrate / fish / salmonid WGDs, building paranome and Ks-age mixture models, applying KsRates substitution-rate correction across lineages, or testing alternative biased-fractionation / dosage-balance models post-WGD.

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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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Normalizes ChIP-seq data using exogenous spike-in (ChIP-Rx with Drosophila chromatin per Orlando 2014 / Egan 2016; E. coli carryover for CUT&RUN/CUT&Tag). Distinguishes RRPM from Rx-Input scaling, integrates with DiffBind / DESeq2 / edgeR / csaw via sizeFactors and DiffBind library-size vectors, applies the Patel et al 2024 *Nat Biotechnol* failure-mode framework, and validates that normalization is applied at the read level (not peak counts). Use when global signal shifts are expected (HDACi, BETi, EZH2i, dosage, target knockdown), when ChIPseqSpikeInFree detects post-hoc shifts, or when validating internal-control regions before publication.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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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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This skill should be used when user asks to "use supabase-js", "query Supabase database", "supabase auth", "supabase storage", "supabase realtime", "supabase edge functions", or works with the @supabase/supabase-js JavaScript/TypeScript SDK.

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This skill should be used when user asks to "use supabase CLI", "supabase init", "supabase start", "run migrations", "deploy edge functions", "manage Supabase project", or works with the supabase command-line tool for local development and project management.

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Load this first for any task involving images, pictures, photos, scans, frames, volumes, or visual data — including reading, writing, filtering, enhancing, denoising, sharpening, deblurring, thresholding, segmenting, masking, detecting, finding or counting objects, removing backgrounds, measuring, comparing, registering, stitching, aligning, cropping, resizing, transforming, or analyzing. Use for image I/O (TIFF, PNG, JPEG, RAW, HDR), histograms, edge detection, color processing, morphology, geometric transforms, deep learning for images, quality assessment, and 3-D volume processing. Also triggers when users describe image problems (dark, noisy, blurry, low contrast, uneven lighting, hazy, color cast) or data exploration tasks (folder of images, characterize data, understand format). Handles microscopy (cells, particles) and general scientific imaging. Routes to sibling skills for medical imaging (DICOM, NIfTI), hyperspectral data, and visual inspection.

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Deploy frontend and full-stack apps on Vercel with previews, edge functions, environment promotion, and production guardrails. Use when shipping Next.js, SvelteKit, or static sites with zero-config CI/CD.

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Create operational runbooks and standard operating procedures. Document troubleshooting guides and recovery procedures. Use when documenting operational knowledge.

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Gather external knowledge the spec needs and distill it into §R — the durable research log — so build grounds in facts instead of hallucinating library behavior. Each finding cites a source; unsourced claims are flagged, never written as fact. Triggers when a spec decision hinges on a library/API/best practice the agent is unsure of, when the user says "research this", "what's the best lib for…", "check current best practice", or invokes /ck:research. Defers the §R write to the spec skill.

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Generate comprehensive edge cases and test scenarios by decomposing features across 12 dimensions. Use before implementation or testing to catch issues early.

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Answer a question from a second-brain vault by reading its own pages, citing the pages used, and saying plainly when the vault does not contain the answer. Use this skill whenever the user asks what they know about a topic, what they have read on something, what connects two ideas, what they have changed their mind about, or asks any question that should be answered from their own notes rather than general knowledge. Do NOT use for ingesting new material, for general questions the vault has nothing to do with, or when the user explicitly wants an answer from the open web.

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Reduce defensive writing in drafts and revisions by removing unnecessary caveats, disclaimers, hedges, apology-like framing, negative self-limiting statements, and over-explanations while preserving necessary scope, accuracy, safety, legal, ethical, and methodological limits. Use when drafting or revising academic writing, papers, essays, abstracts, introductions, contribution statements, discussions, conclusions, technical explanations, grant writing, product writing, policy writing, professional reports, or any text the user wants to be clearer, stronger, more direct, more concise, more confident, less verbose, less caveated, less apologetic, or less defensive.

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Render the multi-agent orchestration DAG for a session — parent→child subagent edges, tree depth, and fan-out — from the Agent Monitor workflow intelligence API. Cross-checks the orchestration dataset against the raw agent records and session detail. Use when visualizing how a session's agent structure was organized.

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Build conversational AI voice agents on the ElevenLabs platform. Configure agent + tools + knowledge base, integrate SDK (React / React Native / Swift / JS / server-side), test, deploy. Use whenever the user mentions ElevenLabs, building a voice agent, an AI phone system, an AI receptionist, conversational AI, or troubleshooting deprecated @11labs packages, webhook errors, CSP violations, localhost allowlist, or tool parsing errors.

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Transforms workflow to use Manus-style persistent markdown files for planning, progress tracking, and knowledge storage. Use when starting complex tasks, multi-step projects, research tasks, or when the user mentions planning, organizing work, tracking progress, or wants structured output.

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