User Guide Overview

CLAIREscope is organized into modular exploratory studios accessible via the top navigation tabs:

1. 🎨 Static UMAP Grid: Side-by-side sample and global expression grids with Loupe-like dynamic contrast controls and bottom legend wrapping.
2. ✨ Interactive UMAP: Hardware-accelerated Plotly 2D/3D WebGL scatter viewer with lasso selection, auto-highlighting, and camera persistence.
3. 📊 Sample Composition: Proportional donut charts and cell-state stacked distributions with Fisher's exact / Chi-square test statistics.
4. 🎻 Gene Expression Violins: Multi-gene distribution violins with automated Mann-Whitney U test p-values.
5. 📈 Signature & Pathway Scoring: Built-in score generator for custom gene sets and cutaneous biology signatures.
6. 🎯 Correlation & Scatter: Bivariate co-expression scatter plots with linear regression and Pearson / Spearman correlation statistics.
7. 🌿 Trajectory Analysis: Diffusion Pseudotime (DPT) curves, vector trajectories, and precomputed figure galleries.
8. 🌋 Differential Expression: Interactive volcano plots with customizable fold-change and p-value cutoffs.
9. 🧬 Pathway Enrichment: Hypergeometric over-representation analysis against curated Gene Ontology and pathway databases.
10. 🔥 Expression Heatmap Studio: Publication-grade hierarchical clustered heatmaps with Z-score standardization.