| Deposited data |
|
| scRNA-seq data of mouse brain cortex |
Zeisel et al.39
|
GEO: GSE60361
|
| 10x Visium data of mouse brain cortex (free frozen) |
10x Genomics |
https://www.10xgenomics.com/resources/datasets/mouse-brain-section-coronal-1-standard-1-0-0 |
| 10x Visium data of mouse brain cortex (FFPE) |
10x Genomics |
https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0 |
| scRNA-seq data of mouse kidney |
Wu et al.47
|
GEO: GSE119531
|
| SRT data of mouse kidney (FFPE) |
10x Genomics |
https://www.10xgenomics.com/resources/datasets/adult-mouse-kidney-ffpe-1-standard-1-3-0 |
| ST and paired scRNA-seq data of PDAC |
Moncada et al.30
|
GEO: GSE111672
|
| MERFISH data of mouse brain cortex |
Zhuang et al.68
|
https://cellxgene.cziscience.com/collections/31937775-06024e52-a799-b6acdd2bac2e |
| Stereo-seq data of mouse brain cortex |
STOmicsDB70
|
https://db.cngb.org/stomics/datasets/STDS0000234 |
| 10x Visium data of human breast cancer |
Wu et al.58
|
GEO: GSE176078
|
|
| Software and algorithms |
|
| R (v4.1.3) |
R Core Team |
https://www.r-project.org/ |
| Python (v3.9.7) |
Python Software Foundation |
https://www.python.org/ |
| CARD (v1.0) |
Ma et al.31
|
https://github.com/YMa-lab/CARD |
| Seurat (v4.3.0) |
Butler et al.24
|
https://satijalab.org/seurat |
| Giotto (v1.1.0) |
Dries et al.25
|
https://github.com/RubD/Giotto/ |
| Squidpy (v1.2.2) |
Palla et al.26
|
https://squidpy.readthedocs.io/en/stable/ |
| Scanpy (v1.9.1) |
Wolf et al.27
|
https://scanpy.readthedocs.io/en/stable/ |
| Cell2Location (v0.1) |
Kleshchevnikov et al.16
|
https://github.com/BayraktarLab/cell2location |
| Stlearn (v0.4.6) |
Pham et al.14
|
https://github.com/BiomedicalMachineLearning/stLearn |
| SpaGCN (v1.2.2) |
Hu et al.12
|
https://github.com/jianhuupenn/SpaGCN |
| BayesSpace (v1.4.1) |
Zhao et al.11
|
https://github.com/edward130603/BayesSpace |
| SEDR (v1.0.0) |
Fu et al.13
|
https://github.com/JinmiaoChenLab/SEDR |
| MENDER (v1.1) |
Yuan25
|
https://github.com/yuanzhiyuan/MENDER |
| BASS (v1.1.0.016) |
Li and Zhou24
|
https://github.com/zhengli09/BASS |
| SPOTlight (v0.99.8) |
Elosua-Bayes et al.19
|
https://github.com/MarcElosua/SPOTlight |
| StereoScope (v0.3) |
Andersson et al.18
|
https://github.com/almaan/stereoscope |
| RCTD (v2.0.0) |
Cable et al.17
|
https://github.com/dmcable/spacexr |
| SPROD (v1.0) |
Wang et al.34
|
https://github.com/yunguan-wang/SPROD |
| SPCS (inline) |
Liu et al.36
|
https://github.com/Usos/SPCS |
| SpotClean (v0.99.2) |
Ni et al.33
|
https://github.com/zijianni/SpotClean |
| SCDD (v1.0.0) |
Liu et al.35
|
https://github.com/lyotvincent/SCDD |
| Matplotlib (v3.5.1) |
Matplotlib development team |
https://matplotlib.org |
| De-spot (v1.0.0) |
This paper |
https://zenodo.org/doi/10.5281/zenodo.12742999 |
