Awesome Spatial Transcriptomics
A curated list of methods, software, foundation models, data resources and tutorials for spatial transcriptomics and the single-cell analyses it relies on, with each entry checked against its paper and code.
Methods and sources
Scope
Methods, software, foundation models, data and learning materials for spatial transcriptomics, plus the single-cell methods that spatial analyses build on. Most software is listed with its paper; preprints are marked.
Ordering
Sections follow the steps in Figure 1, and software within a section is ordered by GitHub stars. Where independent benchmarks exist, they are listed under the section heading.
Verification
Every link, repository and DOI is checked automatically, and every description against its paper and documentation.
Sources
Stars and last commits come from GitHub, citation counts from Crossref.