CellScape

CellScape visualizes single-cell genomic data and phylogenetic relationships to analyze clonal evolution in heterogeneous cell populations.

Key Features:

• Single-Cell Phylogeny Visualization: Displays evolutionary relationships among individual cells using phylogenetic trees provided as edge lists.
• Genomic Heatmap Integration: Links phylogenetic structures with heatmaps representing locus-specific mutation calls or copy-number states for each cell.
• Flexible Phylogeny Representation: Supports multiple phylogenetic formats including dendrograms and evolutionary trees with observed or latent internal nodes.
• Copy Number and Mutation Data Support: Processes per-cell genomic profiles derived from copy-number segmentation or targeted mutation calls.

Scientific Applications:

• Single-Cell Cancer Evolution Analysis: Investigates clonal evolution, mutation accumulation, and lineage diversification in tumor cell populations.
• Genomic Heterogeneity Studies: Examines variation in mutation and copy-number states across individual cells.
• Phylogenetic Interpretation of Single-Cell Data: Integrates genomic profiles with evolutionary trees to study tumor progression, treatment resistance, and metastatic dissemination.

Methodology:

CellScape integrates per-cell genomic profiles such as copy-number segment data or targeted mutation calls with a single-cell phylogeny provided as an edge list, and generates synchronized visualizations combining phylogenetic trees with genomic heatmaps representing mutation or copy-number states across cells.