Table 1 Benchmark tools and datasets
From: Benchmarking clustering, alignment, and integration methods for spatial transcriptomics
Algorithm | Task | Language | Resource | Output | Method | Link |
BANKSY | Clustering | R | Singhal et al. 2024Â [21] | Clustering Labels, Embedding | Azimuthal Gabor filter | |
ADEPT | Clustering | Python | Hu et al. 2023 [28] | Clustering Labels, Embedding | Graph Autoencoder, Imputation, Differentially Expressed Genes | |
GraphST | Clustering | Python | Long et al. 2022 [4] | Clustering Labels, Embedding | Graph Neural Network, Contrastive Learning | |
SpaceFlow | Clustering | Python | Ren et al. 2022 [27] | Clustering Labels, Embedding | Spatially Regularized Deep Graph Infomax | |
conST | Clustering | Python | Zong et al. 2022 [25] | Clustering Labels, Embedding | Contrastive Learning, Masked Autoencoder | |
ConGI | Clustering | Python | Zeng et al. 2022 [26] | Clustering Labels, Embedding | Contrastive Learning, Autoencoder | |
SpatialPCA | Clustering | R | Shang et al. 2022 [19] | Clustering Labels | Spatial Probabilistic PCA | |
DR.SC | Clustering | R | Liu et al. 2022 [20] | Clustering Labels | Regression Analysis, Imputation | |
STAGATE | Clustering | Python | Dong et al. 2022 [3] | Clustering Labels, Embedding | Graph Autoencoder, Attention Mechanism | |
CCST | Clustering | Python | Li et al. 2022 [24] | Clustering Labels, Embedding | Graph Convolutional Network | |
SEDR | Clustering | Python | Fu et al. 2021 [23] | Clustering Labels, Embedding | Deep Autoencoder, Graph Variational Autoencoder | |
SpaGCN | Clustering | Python | Hu et al. 2021 [22] | Clustering Labels | Graph Convolutional Network | |
BayesSpace | Clustering | R | Li et al. 2021 [17] | Clustering Labels | Markov chain Monte Carlo, Differentially Expressed Genes | |
STalign | Alignment | Python | Clifton et al. 2023 [36] | Refined Coordinates | Diffeomorphic Metric Mapping | |
GPSA | Alignment | Python | Jones et al. 2023 [37] | Refined Coordinates | Gaussian Process | |
SPIRAL | Integration | Python | Guo et al. 2023 [42] | Refined Coordinates, Embedding | GraphSAGE, Optimal Transport | |
STAligner | Integration | Python | Zhou et al. 2023 [39] | Embedding | Graph Autoencoder, Attention Mechanism, Triplet Loss | |
PASTE | Alignment Integration | Python | Zeira et al. 2022 [33] | Alignment Matrix, Integrated Slice, 3D Reconstruction | Fused Gromov-Wasserstein Optimal Transport, Generalized Procrustes Analysis | |
PASTE2 | Alignment Integration | Python | Xinhao et al. 2022 [34] | Partial Alignment Matrix, 3D Reconstruction | Partial Fused Gromov-Wasserstein Optimal Transport, Generalized Procrustes Analysis | |
PRECAST | Clustering Integration | R | Liu et al. 2023 [41] | Embedding | Gaussian Mixture Model, Discrete Hidden Markov Random Field | |
SPACEL | Deconvolution Clustering Alignment | Python | Xu et al. 2023 [35] | Cell Type Composition, Refined Coordinates, 3D Reconstruction | Variational Autoencoder, Graph Convolutional Network, Adversarial Learning, Regression | |
BASS | Clustering Integration | R | Li et al. 2022 [18] | Clustering Labels | Bayesian Analysis, Multi-sample Analysis | |
DeepST | Clustering Integration | Python | Xu et al. 2022 [40] | Embedding | Data Augmentation, Variational graph autoencoder | |
ST dataset | ST type | Abbreviations | ST protocol | Spots/genes | Num. of used slices | Source |
Dataset 1: Human Dorsal Lateral Prefrontal Cortex data [43] | Sequencing-based | DLPFC | 10x Visium | 3431-4788/33,538 | 12 | |
Dataset 2: Human Breast Cancer Block A Section 1 [44] | Sequencing-based | HBCA1 | 10x Visium | 3798/36,601 | 1 | |
Dataset 3: Mouse Brain Section 2 Sagittal Anterior [45] | Sequencing-based | MB2SA | 10x Visium | 2695/32,285 | 2 | |
Dataset 4: HER2 Positive Breast Tumors [46] | Sequencing-based | HER2BT | Spatial Transcriptomics | 177-692/ 14,861-15,701 | 8 | |
Dataset 5: Mouse Hippocampus [47] | Sequencing-based | MHPC | Slide-seq v2 | 41,770/23,264 | 1 | https://singlecell.broadinstitute.org/single_cell/study/SCP815 |
Dataset 6: MOSTA Embryo [48] | Sequencing-based | Embryo | Stereo-seq | 30,124-51,365/26,854-27,810 | 2 | |
Dataset 7: Mouse Visual Cortex [9] | Sequencing-based | MVC | STARmap | 1207/1020 | 1 | |
Dataset 8: Mouse Prefrontal Cortex [9] | Sequencing-based | MPFC | STARmap | 1049-1088/166 | 3 | https://github.com/zhengli09/BASS-Analysis/blob/master/data/STARmap_mpfc.RData |
Dataset 9: Mouse Hypothalamus [49] | Imaging-based | MHypo | MERFISH | 5488-5926/155 | 5 | https://datadryad.org/stash/dataset/doi:10.5061/dryad.8t8s248 |
Dataset 10: Mouse Brain [50] | Sequencing-based | MB | MERFISH | 2033-7626/254 | 33 |