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Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.
Create publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and network graphs. Use when generating figures for repertoire comparisons, clonal dynamics, or V(D)J gene usage.
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 dist...
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...
End-to-end flow, spectral, and mass cytometry (CyTOF) pipeline from raw FCS files to differentially abundant/expressed cell populations. Orchestrates the read -> compensate/unmix -> transform -> QC -> doublet-removal -> cluster-or-gate -> annotate -> diffcyt DA/DS chain with flowCore/CATALYST/dif...
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
Create publication-ready volcano plots with custom thresholds, gene labels, and highlighting using ggplot2, EnhancedVolcano, or matplotlib. Use when visualizing differential expression or association results with gene annotations.
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.
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