811 skills · sorted by relevance
Render music videos from audio files and lyrics using Remotion. Accepts audio + LRC/JSON lyrics + title to produce MP4 videos with waveform visualization and synced lyrics display. Use when users mention MV generation, music video rendering, creating video from audio/lyrics, or visualizing songs.
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Use when working with *.excalidraw or *.excalidraw.json files, user mentions diagrams/flowcharts, or requests architecture visualization - delegates all Excalidraw operations to subagents to prevent context exhaustion from verbose JSON (single files: 4k-22k tokens, can exceed read limits)
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Expert interior designer with deep knowledge of space planning, color theory (Munsell, NCS), lighting design (IES standards), furniture proportions, and AI-assisted visualization. Use for room layout optimization, lighting calculations, color palette selection for interiors, furniture placement, style consultation. Activate on "interior design", "room layout", "lighting design", "furniture placement", "space planning", "Munsell color". NOT for exterior/landscape design, architectural structure, web/UI design (use web-design-expert), brand color theory (use color-theory-palette-harmony-expert), or building codes/permits.
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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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Guides product-design decisions using the consuming repository's design-system, product, and repository context. Use when designing UI, choosing layout or navigation, handling states and forms, messaging, disclosure, onboarding, visualization, copy, delete, filter, or search interactions. Triggers on 'design guidance', 'how to design', 'UI pattern', 'product design', 'scenario pattern', 'confirmation dialog', 'delete flow', 'copy to clipboard', 'filter', and 'search'.
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Trigger when: (1) the user mentions "manim", "scene", "video", "EN/KO render", "GEODE_HERO_LANG", "1080p60", or (2) editing files under `scripts/visualizations/` ending in `.py`, or (3) the user asks to render, re-render, or extend any of the four validated scenes (`geode_hero.py`, `autoresearch_filewalk.py`, `autoresearch_compare.py`, `critical_floor.py`). GEODE Manim Scene authoring standard. Locks the patterns the four validated scenes already share — Anthropic-style palette, Helvetica Neue + Pretendard font pairing with weight=NORMAL, EN/KO multilingual lang via `GEODE_HERO_LANG` env, `_dashed_arrow_with_head` stage-coupled tinting, `verify_hero_layout.py` ratchet — so the next scene does not re-discover the kerning / padding / transition regressions catalogued in [[viz-frame-audit]].
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Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.
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Unsupervised clustering and cell-type identification for high-dimensional flow, spectral, and mass cytometry - FlowSOM, PhenoGraph, FlowSOM-via-CATALYST, with UMAP/tSNE for visualization. Covers the type-vs-state marker distinction (cluster on lineage, test state within clusters), over-provision-then-metacluster, the Weber-Robinson benchmark, seed dependence and metacluster stability, why embeddings are for looking not measuring, and median-heatmap annotation/merging. Use when discovering populations without predefined gates, choosing a clustering algorithm, selecting the number of metaclusters, or annotating clusters into cell types.
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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.
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Add p-value brackets, significance asterisks, and effect-size annotations to distribution plots using ggpubr, ggsignif, and statannotations with correct test selection (parametric vs non-parametric vs paired), multiple-testing adjustment, and rendering of negative results. Use when a boxplot/violin/raincloud needs in-figure statistical comparisons between groups.
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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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Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling, and LD-aware regional rendering. Use when visualizing association results across the genome, comparing two traits, computing genomic inflation lambda, or zooming into a locus with LD coloring.
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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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Build clustered heatmaps for expression matrices and other features-by-samples data with rigorous distance/linkage/scaling choices, robust color mapping, optimal leaf ordering, and ComplexHeatmap/pheatmap/seaborn rendering. Covers the ward.D vs ward.D2 trap, the row-vs-column scaling decision, multi-track annotations, oncoPrint, and raster rendering for large matrices. Use when visualizing expression patterns across samples or identifying co-regulated clusters.
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Build sequence logos from aligned DNA, RNA, or protein motifs using ggseqlogo (R), Logomaker (Python), or WebLogo with explicit bits vs probability encoding, background-frequency correction, custom alphabets, and multi-logo stacking. Use when visualizing motif PWMs (TF binding, splice sites, CRISPR spacers), aligned-position composition, or comparing two motif sets.
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Build publication-quality figures in R with ggplot2 using the grammar of graphics (data + aesthetics + geometries + scales + facets + themes) with CVD-safe palettes, cairo_pdf TrueType embedding, programmatic aes via tidy evaluation, and the theme_classic publication baseline. Use when producing static figures in R for papers, presentations, or reports.
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Compose multi-panel publication figures with patchwork, cowplot, gridExtra (R), or matplotlib GridSpec/subfigures (Python) including shared axes/legends/guides collection, panel labels in Nature/Cell convention, and journal-spec sizing. Covers patchwork ≥1.2.0 axes='collect' feature, Type-42 font embedding, and the cairo_pdf save path. Use when composing 2+ subpanels into a single figure for journal submission.
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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 publication-quality figures with matplotlib using the object-oriented Figure/Axes API, constrained_layout, rcParams customization, TrueType (Type-42) font embedding for journal submission, and CVD-safe palettes. Covers seaborn integration, common chart types, axis formatting, and the small gotchas that distinguish reproducible matplotlib from notebook scratch. Use when producing publication figures in Python — RNA-seq scatter, single-cell embeddings, generic biological plotting.
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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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Plot per-gene mutation distributions on a protein-domain map (lollipop / needle plots) showing mutation position, recurrence count, and variant classification with maftools, g3-lollipop, trackViewer, and ProteinPaint. Use when visualizing recurrent mutation hotspots on a single gene's protein, marking domain boundaries from UniProt/Pfam, comparing missense vs truncating distributions, or contrasting two cohorts on the same lollipop.
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Build UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.
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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.
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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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