「visualization」の検索結果

Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).

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Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.

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Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions), hyperparameter sensitivity, and the well-documented limits of 2D embeddings. Covers PCA biplot/scree/loadings, t-SNE PCA initialization (Kobak-Berens 2019), UMAP n_neighbors/min_dist trade-offs, and the Chari-Pachter 2023 critique. Use when visualizing high-dimensional data — bulk PCA, single-cell embeddings, multi-omics integration projections.

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Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

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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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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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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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End-to-end copy number variant detection workflow from BAM files. Covers CNVkit analysis for exome/targeted sequencing with visualization and annotation. Use when detecting copy number alterations from sequencing data.

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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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Select colormaps and qualitative palettes for scientific figures using perceptual-uniformity, color-vision-deficiency safety, and luminance-monotonicity criteria. Covers Crameri scientific colormaps, viridis/cividis/magma, Okabe-Ito categorical, ColorBrewer, and the rainbow/jet critique. Use when choosing palettes for heatmaps, scatter, networks, or any encoding where color carries quantitative or categorical meaning.

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Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.

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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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Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq.

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Workflow for enrichment testing, ranked-gene analysis, pathway scoring, and pathway-focused visualization across omics outputs.

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Workflow for RNA modification analysis such as m6A peak calling, differential modification, and transcript-level visualization.

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Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.

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Workflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.

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Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.

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Generate Mermaid architecture diagrams from your codebase. Produces C4 context and container diagrams, sequence diagrams for key flows, ER diagrams from database schemas, and module dependency graphs. Use when you need architecture diagrams, system diagrams, database ERD, sequence diagrams, dependency visualization, or C4 model diagrams.

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Creates interactive data visualizations with Apache ECharts, the open-source JavaScript charting library. Use when a user asks to build charts, dashboards, or data-driven graphics using ECharts in React, Vue, or vanilla JavaScript applications, render a chart to SVG on the server, or upgrade from ECharts 5 to 6.

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Manipulate colors with chroma.js — convert between color spaces (RGB, HSL, LAB, LCH), generate palettes and scales, mix and blend colors, check contrast ratios, and build accessible color systems. Use when tasks involve creating color palettes, theming, accessibility checks, or data visualization color scales.

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Covers scripting Autodesk 3ds Max, the 3D modeling and rendering application, with MAXScript and Python (pymxs): scene manipulation, object creation, material assignment, camera and light setup, batch operations, and file I/O. Use when tasks involve automating repetitive 3ds Max workflows, batch processing scenes, running scripts headless with 3dsmaxbatch, creating custom tools, or scripting scene setup for archviz, product visualization, or VFX.

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World-class color theory expertise combining the scientific precision of Josef Albers' "Interaction of Color," the systematic thinking of color systems from Pantone and RAL, and the perceptual psychology insights from researchers like Bevil Conway. Color is not just aesthetics - it's communication, emotion, and usability compressed into wavelengths. Great color work is invisible when done right. Users don't notice "nice colors" - they notice when they can't read text, when buttons don't look clickable, when errors don't feel urgent, or when the interface feels "off" without knowing why. Color theory is the science of making the right thing feel obvious. Use when "color theory, color palette, color scheme, color harmony, complementary colors, analogous colors, contrast ratio, dark mode colors, light mode, color tokens, semantic colors, color accessibility, color blindness, color psychology, color system, brand colors, data visualization colors, color, design, accessibility, contrast, dark-mode, theming, tokens, wcag, palette, harmony" mentioned.

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