Results for “visualization”

Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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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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Detect syntenic blocks and structural rearrangements between genomes using MCScanX (Wang 2012), JCVI/MCScan (Tang 2008 Python), GENESPACE (Lovell 2022) for orthology-anchored riparian visualization, SyRI for structural variation, AnchorWave for sequence-level synteny, i-ADHoRe 3.0 for highly diverged species, SynNet for synteny networks, and ntSynt for multi-genome macrosynteny. Use when identifying collinear gene blocks across species, distinguishing macrosynteny from microsynteny, detecting inversions/translocations/duplications, anchoring orthology in WGD lineages, producing publication riparian plots, computing synteny block age via Ks (cross-references whole-genome-duplication), or running synteny-aware ortholog inference in polyploids.

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

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Segments the genome into chromatin states from combinatorial histone modification and chromatin factor ChIP-seq data. Uses ChromHMM (multivariate HMM on binarized signal, v1.27), Segway (Dynamic Bayesian Network on continuous signal), EpiSegMix (flexible-distribution HMM with duration modeling, 2024), EpiLogos (multi-biosample visualization), IDEAS (cell-type-aware joint), and full-stack ChromHMM (Vu Ernst 2022) for cross-cell-type segmentations. Handles state-count selection (15 vs 18 vs 25 states), binarization choice, OverlapEnrichment / NeighborhoodEnrichment downstream analysis, and cross-biosample integration. Use when learning chromatin states from a histone mark panel, characterizing learned states by genomic feature enrichment, or comparing chromatin landscapes across cell types.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Expert landscape designer transforming yards through photo mapping, 3D visualization, seasonal planning, and deep plant knowledge. Specializes in fast-growing privacy screens (knows arborvitae pitfalls), architecture-appropriate design, outdoor living spaces, and realistic maintenance expectations. Activate on "landscape design", "yard design", "garden planning", "plant selection", "privacy screen", "outdoor living", "backyard makeover", "arborvitae", "hedge", "fast growing tree", "landscaping ideas". NOT for interior design (use interior-design-expert), hardscape construction (consult contractors), or lawn care chemicals (consult local experts).

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Design and build mathematically rigorous, high-density, interactive data graphics and streaming telemetry visualizations following Mike Bostock's D3.js and Observable methodologies. Use when crafting custom SVG/Canvas charts, reactive streaming time-series, multi-dimensional brush-and-link coordinates, small multiples, or topological swarm graphs. NOT for generic dashboard template clones, basic spreadsheet charts, or off-the-shelf low-effort wrapper libraries.

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Build or improve a Coval dashboard with metric visualizations backed by real data. Creates new dashboards from scratch or rebuilds existing ones by analyzing usage patterns, metric frequency, and data density. Use when user says "create a dashboard", "build a dashboard", "improve my dashboard", "add widgets", "visualize my metrics", "make a performance dashboard", or "dashboard for my runs".

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SERP-based semantic topic clustering for content architecture planning. Groups keywords by actual Google SERP overlap (not text similarity), designs hub-and-spoke content clusters with internal link matrices, and generates interactive visualizations. Optionally executes content creation if claude-blog is installed. Use when user says "topic cluster", "content cluster", "semantic clustering", "pillar page", "hub and spoke", "content architecture", "keyword grouping", or "cluster plan".

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Custom chat display for an MCP or agent tool's result, DB-loaded from tool_ui by default. Use when adding or customizing a tool visualization, making a tool result look good, rendering MCP tool output, or authoring a renderer for a tool that shows the generic view.

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在MATLAB绘制的直方图上叠加标记局部峰值，不显示文本标签，并支持自定义标记样式（如蓝色实心倒三角）。

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Creates interactive educational MicroSims using the best-matched JavaScript library (p5.js, Chart.js, Plotly, Mermaid, vis-network, vis-timeline, Leaflet, Venn.js). Analyzes user requirements to route to the appropriate visualization type and generates complete MicroSim packages with HTML, JavaScript, CSS, documentation, and metadata.

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Transform data into compelling narratives using visualization, context, and persuasive structure. Use when presenting analytics to stakeholders, creating data reports, or building executive presentations.

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Maxim 3D CGI product render — engineered for purchase confidence and premium positioning. Uses Material Realism + Endowment Effect + Photorealism Trust Signals to move premium-product viewers toward purchase. Use for luxury product reveals, architectural visualization, tech hardware marketing, high-ticket commerce.

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Maxim Presentation Intelligence — pitch decks, investor presentations, executive briefings, product demos, conference talks, narrative-driven visual storytelling, data visualization in slides. Applies Minto Pyramid, Duarte Sparkline, McKinsey Slide Logic, and Dual Coding Theory to every deck. Powered by Maxim behavioral science layer.

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Power BI report visualization design prompt for creating effective, user-friendly, and accessible reports with optimal chart selection and layout design.

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Comprehensive technology-agnostic prompt for analyzing and documenting project folder structures. Auto-detects project types (.NET, Java, React, Angular, Python, Node.js, Flutter), generates detailed blueprints with visualization options, naming conventions, file placement patterns, and extension templates for maintaining consistent code organization across diverse technology stacks.

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Index a codebase with GitNexus and serve an interactive knowledge graph via web UI + Cloudflare tunnel.

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Audio spectrograms/features (mel, chroma, MFCC) via CLI.

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Generate flat, minimal light/dark-aware SVG diagrams as standalone HTML files, using a unified educational visual language with 9 semantic color ramps, sentence-case typography, and automatic dark mode. Best suited for educational and non-software visuals — physics setups, chemistry mechanisms, math curves, physical objects (aircraft, turbines, smartphones, mechanical watches), anatomy, floor plans, cross-sections, narrative journeys (lifecycle of X, process of Y), hub-spoke system integrations (smart city, IoT), and exploded layer views. If a more specialized skill exists for the subject (dedicated software/cloud architecture, hand-drawn sketches, animated explainers, etc.), prefer that — otherwise this skill can also serve as a general-purpose SVG diagram fallback with a clean educational look. Ships with 15 example diagrams.

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Dark-themed SVG architecture/cloud/infra diagrams as HTML.

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Hand-drawn Excalidraw JSON diagrams (arch, flow, seq).

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