  Human and animal tissues consist of heterogeneous cell types that organize
and interact in highly structured manners. Bulk and single-cell sequencing
technologies remove cells from their original microenvironments, resulting in a
loss of spatial information. Spatial transcriptomics is a recent technological
innovation that measures transcriptomic information while preserving spatial
information. Spatial transcriptomic data can be generated in several ways. RNA
molecules are measured by in situ sequencing, in situ hybridization, or spatial
barcoding to recover original spatial coordinates. The inclusion of spatial
information expands the range of possibilities for analysis and visualization,
and spurred the development of numerous novel methods. In this review, we
summarize the core concepts of spatial genomics technology and provide a
comprehensive review of current analysis and visualization methods for spatial
transcriptomics.
