SpatialFlux: an R package for distance gradient analysis in spatial transcriptomics

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Spatial transcriptomics (ST) data analysis presents challenges including low sampling, diverse tissue morphology, and high dropout rates.
• Overcoming these limitations is crucial for advancing biological discoveries using ST techniques.

Purpose of the Study:

• To introduce SpatialFlux, an R package designed for reference-based distance gradient analysis in ST data.
• To provide tools for identifying and visualizing differentially expressed genes and pathways across multiple ST tissue sections.

Main Methods:

• Development of SpatialFlux, an R package utilizing reference-based distance gradient analysis.
• Implementation of unbiased and biased approaches for gene and pathway identification.
• Visualization of expression patterns along various axes within ST data.

Main Results:

• SpatialFlux effectively addresses inherent limitations of ST data analysis.
• The package facilitates comprehensive identification and visualization of differential gene expression.
• Enables analysis across multiple tissue sections and along defined spatial axes.

Conclusions:

• SpatialFlux overcomes key challenges in spatial transcriptomics data analysis and visualization.
• The package supports continued biological discovery by providing robust analytical tools.
• Facilitates deeper understanding of spatial gene expression patterns in complex biological systems.