TABLE 1.
Summary for algorithms designed for spatial omics analysis
| Name | Usage | Environment | URL |
|---|---|---|---|
| SCTransform | Data preprocessing | R | https://github.com/ChristophH/sctransform |
| Giotto | Data preprocessing, spatial variable gene identification, cell identity inference, cell–cell crosstalk modelling, clustering analysis | R | http://spatialgiotto.rc.fas.harvard.edu/giotto.html |
| Seurat | Data preprocessing, spatial variable gene identification, cell identity inference, clustering analysis | R | https://satijalab.org/seurat/vignettes.html |
| SpatialDE | Spatial variable gene identification | Python | https://github.com/Teichlab/SpatialDE |
| trendsceek | Spatial variable gene identification | R | https://github.com/edsgard/trendsceek |
| scGCO | Spatial variable gene identification | Python | https://github.com/WangPeng‐Lab/scGCO |
| SPARK | Spatial variable gene identification | R | https://github.com/xzhoulab/SPARK |
| SOMDE | Spatial variable gene identification | Python | https://pypi.org/project/somde/ |
| BayesSpace | Clustering analysis | R | http://www.bioconductor.org/packages/release/bioc/html/BayesSpace.html |
| SpatialCPie | Clustering analysis | R | https://www.bioconductor.org/packages/release/bioc/html/SpatialCPie.html |
| SPOTlight | Cell identity inference/deconvolution | R | https://github.com/MarcElosua/SPOTlight |
| RCTD | Cell identity inference/deconvolution | R | https://github.com/dmcable/RCTD |
| stereoscope | Cell identity inference/deconvolution | Python | https://github.com/almaan/stereoscope |
| DSTG | Cell identity inference/deconvolution | Python | https://github.com/Su‐informatics‐lab/DSTG |
| STUtility | Data preprocessing, spatial variable gene identification, clustering analysis, tissue segmentation, image processing | R | https://ludvigla.github.io/STUtility_web_site/index.html |
| Squidpy | Data preprocessing, spatial variable gene identification, cell identity inference, cell–cell crosstalk modelling, clustering analysis, tissue segmentation | Python | https://github.com/theislab/squidpy |
| Baysor | Tissue segmentation | Linux | https://github.com/kharchenkolab/Baysor |
| SPATA | Tissue segmentation, trajectory modelling | R | https://themilolab.github.io/SPATA/index.html |
| stLearn | Trajectory modelling; cell–cell crosstalk modelling | Python | https://stlearn.readthedocs.io/en/latest/ |
| GCNG | Cell–cell crosstalk modelling | Python | https://github.com/xiaoyeye/GCNG |
| SpaOTsc | Cell–cell crosstalk modelling | Python | https://github.com/zcang/SpaOTsc |
| MISTy | Cell–cell crosstalk modelling | R | https://github.com/saezlab/mistyR |