🔬 CLAIREscope: Cellular Landscape Analysis, Interpretation & Results Explorer

CLAIREscope is a unified, publication-grade interactive single-cell analysis platform designed for exploratory transcriptomics, multi-project switching, developmental trajectory kinetics modeling, on-the-fly functional genomics, and automated multi-panel export.

🎬 Interactive Tour: Watch the 2-Minute Video Demonstration to see CLAIREscope's real-time analysis studios in action.

🌟 Key Capabilities

🚀 Dynamic Multi-Project Switching: Instantly switch between heterogeneous single-cell cohorts (e.g. multi-condition scRNA-seq, spatial transcriptomics) with on-demand memory management.
🗺️ Publication-Grade Isometric Visualizations: 1:1 aspect ratio UMAPs with Loupe-like dynamic range contrast anchors, customizable colormaps, and one-click 300 DPI SVG/PNG/PDF downloads.
🌿 Continuous Trajectory Expression Drawing Studio: Multi-gene overlay kinetics along Diffusion Pseudotime (DPT), within-sample scaling, and landmark alignment.
🌋 Differential Expression & Volcano Studio: Bidirectional Wilcoxon statistical testing with tunable FDR / Log2(FC) thresholds and live gene labeling.
🔥 Hierarchical Heatmap Studio: Group-averaged or single-cell clustered heatmaps with draggable sortable X-axis ordering and Z-score standardization.
🧬 Pathway Over-Representation Analysis (ORA): Tunable top N up/down gene enrichment across Hallmark and custom signature databases.
📦 Bulk Export & Config Import Studio: Generate comprehensive multi-figure packages and structured 1-row-per-feature CSV matrices with drag-and-drop Excel/CSV configuration importing.

🛠️ Quick Installation & Launch

# Clone the repository
git clone https://github.com/ccneko/CLAIREscope.git
cd CLAIREscope

# Run using uv / Python virtual environment
uv run streamlit run app.py --server.port 8501