Table 2 Representative bioinformatics tools of ST

Tool	Website	Refs
SpatialCPie	https://github.com/jbergenstrahle/SpatialCPie	⁶²
ClusterMap	https://github.com/xgaoo/ClusterMap	⁶³
FICT	https://github.com/haotianteng/FICT	⁶⁴
SpaRTaCo	https://arxiv.org/abs/2110.04872	⁶⁵
SC-MEB	https://github.com/Shufeyangyi2015310117/SC.MEB	⁶⁶
CCST	https://github.com/xiaoyeye/CCST	⁶⁷
SpaCell	https://github.com/BiomedicalMachineLearning/SpaCell	⁶¹
GLISS	https://github.com/junjiezhujason/gliss	⁷²
SpatialDE	https://github.com/Teichlab/SpatialDE	⁶⁸
SOMDE	https://github.com/WhirlFirst/somde	⁶⁹
trendsceek	https://github.com/edsgard/trendsceek	⁷⁰
SPADE	https://github.com/NVlabs/SPADE	⁷¹
SpatialDWLS	https://github.com/rdong08/spatialDWLS_dataset	⁷⁵
DSTG	https://github.com/Su-informatics-lab/DSTG	⁷⁶
DestVI	https://github.com/YosefLab/scvi-tools	⁷⁷
STRIDE	https://github.com/DongqingSun96/STRIDE	⁷⁸
SPOTlight	https://github.com/maciejkula/spotlight	⁷⁴
BayesSpace	https://bioconductor.org/packages/release/bioc/html/BayesSpace.html	⁸¹
XFuse	https://github.com/ludvb/xfuse	⁸⁰
GCNG	https://github.com/xiaoyeye/GCNG	⁸⁴
SVCA	https://github.com/damienArnol/svca	⁸⁵
RCTD	https://github.com/dmcable/RCTD	⁷⁹

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