Schex

Schex implements hexagonal binning to visualize and summarize single-cell RNA-sequencing (scRNA-seq) data by reducing overplotting and representing data density in scatter plots.

Key Features:

• Hexagonal binning: Aggregates points into hexagonal bins to reduce overplotting and represent data density in scatter plots.
• Improved speed and storage efficiency: Uses aggregated hexagonal representations to decrease plotting time and storage requirements for large scRNA-seq datasets.
• Compatibility with SingleCellExperiment and SeuratObject: Accepts SingleCellExperiment and SeuratObject objects for integration into single-cell analysis workflows.

Scientific Applications:

• Exploration of cellular heterogeneity: Visualizes density patterns in scRNA-seq data to support detection of population structure and transcriptional gradients.
• Cell-type identification and marker localization: Highlights regions of high transcriptomic density to aid identification of novel cell types and marker expression patterns.
• Domain-specific studies: Clarifies high-dimensional single-cell patterns for applications in developmental biology, cancer research, and immunology.

Methodology:

Transforms scatter plots into hexagonal-binned plots by aggregating points within each hexagon based on point density to produce heatmap-like density representations.