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

Abstract

Abstract Summary Spatial transcriptomics (ST) data analysis and visualization face several challenges due to low sampling, diversity of tissue morphology and high drop-out inherent to the technique. New analysis methods are needed to overcome these challenges and promote continued biological discoveries. To overcome these constraints, we herein describe SpatialFlux, an R package developed to perform reference-based distance gradient analysis. SpatialFlux allows the identification and comprehensive visualization, in either an unbiased or biased manner, of differentially expressed genes and pathways across multiple ST tissues sections and along various axes, thus overcoming many inherent ST limitations and supporting continued biological discovery. Availability SpatialFlux package source code and vignette are freely available on Github (https://github.com/towerlab/SpatialFlux) and Zenodo (https://zenodo.org/records/21039284).