vissE

vissE performs gene-set analysis and summarizes enriched gene-sets from bulk, single-cell, and spatial omics (including CosMx and Xenium) to enable functional interpretation of complex omics data.

Key Features:

• End-to-End Gene-Set Analysis: Performs gene-set analysis (GSA) from input gene lists or raw single-cell and spatial omics data.
• Versatile Data Handling: Supports bulk, single-cell, and spatial omics data, including sub-cellular localized spatial data from CosMx and Xenium.
• Interactive Visualization: Produces hierarchical visualizations of results at gene, gene-set, and cluster levels using algorithms from the R package vissE.
• Biological Theme Summarization: Identifies and summarizes biological themes by grouping potentially hundreds of significantly enriched gene-sets into semantically interpretable components.

Scientific Applications:

• Functional Genomics: Facilitates functional interpretation of genomic datasets through summarized and visualized gene-set enrichment results.
• Single-Cell and Spatial Omics Research: Analyzes single-cell and spatial omics data to investigate cellular heterogeneity and tissue- or subcellular-specific expression patterns.
• Hypothesis Generation: Highlights enriched biological themes to support generation of hypotheses about underlying biological processes or disease mechanisms.

Methodology:

Implements gene-set analysis (GSA) and gene-set summarization using algorithms from the R package vissE and accepts gene lists or raw single-cell and spatial omics inputs, including CosMx and Xenium.