TABLE I.
A list of relevant methods for the analysis of spatial transcriptomics data. The italicized boldfaced methods are the ones that utilize deep learning (or elements closely aligned). We review these methods in depth in this paper.
| Category | Method | Year | Framework | Language | Software availability |
|---|---|---|---|---|---|
| Spatial reconstruction | Seurat59 | 2015 | Statistical | R | https://github.com/satijalab/seurat |
| novoSpaRc60 | 2019 | Optimization/statistical | Python | https://github.com/rajewsky-lab/novosparc | |
| DEEPsc 61 | 2021 | Machine learning | MATLAB | https://github.com/fmaseda/DEEPsc | |
| Alignment and integration | Spatial backmapping62 | 2015 | Scoring scheme | R | https://github.com/jbogp/nbt_spatial_backmapping |
| Tangram 34 | 2021 | Machine learning | Python | https://github.com/broadinstitute/Tangram | |
| GLUER 63 | 2021 | Machine learning | Python | https://github.com/software-github/GLUER | |
| Spot deconvolution | Stereoscope64 | 2020 | Statistical | Python | https://github.com/almaan/stereoscope |
| DSTG 65 | 2021 | Machine learning | Python, R | https://github.com/Su-informatics-lab/DSTG | |
| SPOTlight66 | 2021 | Machine learning | R | https://github.com/MarcElosua/SPOTlight | |
| RTCD67 | 2021 | Statistical | R | https://github.com/dmcable/RCTD | |
| SpatialDWLS68 | 2021 | Optimization/statistical | R | https://github.com/RubD/Giotto | |
| DestVI 69 | 2021 | Machine learning | Python | https://github.com/YosefLab/scvi-tools | |
| Cell2location70 | 2022 | Statistical | Python | https://github.com/BayraktarLab/cell2location | |
| CARD71 | 2022 | Machine learning | R, C++ | https://github.com/YingMa0107/CARD | |
| Spatial clustering | HMRF72 | 2018 | Statistical | R, Python, C | https://bitbucket.org/qzhudfci/smfishhmrf-py/ |
| SpaCell 73 | 2019 | Machine learning | Python | https://github.com/BiomedicalMachineLearning/SpaCell | |
| StLearn 74 | 2020 | Machine learning | Python | https://github.com/BiomedicalMachineLearning/stLearn | |
| BayesSpace75 | 2021 | Statistical | R, C++ | https://github.com/edward130603/BayesSpace | |
| SpaGCN 76 | 2021 | Machine learning | Python | https://github.com/jianhuupenn/SpaGCN | |
| Spatially variable genes identification | Trendsceek77 | 2018 | Statistial | R | https://github.com/edsgard/trendsceek |
| SpatialDE78 | 2018 | Statistical | Python | https://github.com/Teichlab/SpatialDE | |
| Spark79 | 2020 | Statistical | R, C++ | https://github.com/xzhoulab/SPARK | |
| Cell–cell communication | SpaOTsc80 | 2020 | Machine learning | Python | https://github.com/zcang/SpaOTsc |
| MISTy81 | 2020 | Machine learning | R | https://github.com/saezlab/mistyR | |
| Giotto82 | 2021 | Statistical | R | https://github.com/RubD/Giotto |