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Expand file tree Collapse file tree Original file line number Diff line number Diff line change 8787- [ SpaOTsc] ( https://github.com/zcang/SpaOTsc ) - Spatial imputation via optimal transport
8888- [ Seurat integration workflow] ( https://satijalab.org/seurat/articles/integration_mapping.html ) - Transfer gene expression from scRNA-seq reference
8989- [ Sprod] ( https://www.nature.com/articles/s41592-022-01560-w#Fig2 ) - Spatial denoising method
90+ - [ TISSUE] ( https://github.com/sunericd/TISSUE ) - Transcript imputation with spatial single-cell uncertainty estimation
9091
9192### Bias Correction
9293
187188> (** Smaller** ) Cell types → Cell modules/neighborhoods → Niches/tissue domains (** Larger** )
188189
189190- [ BANKSY] ( https://www.nature.com/articles/s41588-024-01664-3 ) - Unified cell typing and tissue domain segmentation
190- - [ TISSUE] ( https://github.com/sunericd/TISSUE ) - Transcript imputation with spatial single-cell uncertainty estimation
191191- [ CellCharter] ( https://www.nature.com/articles/s41588-023-01588-4 ) - Hierarchical niche detection
192192- [ SpatialGLUE] ( https://www.nature.com/articles/s41592-024-02316-4 ) - Multi-omics cell niche identification
193193- [ smoothclust] ( https://github.com/lmweber/smoothclust ) - Spatial clustering
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