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- For all datasets, we applied the common normalization methods as following.
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Deconvolution of cell types and states in spatial multiomics utilizing TACIT
We curated the cell label by unifying the major cell type annotated by different publications (e.g., considering both “T lymphoid cells” and “T cells” as “T cells”). We neglected the minor cell types, which means those novel subtypes uncovered by scRNA-seq with unsupervised clustering and annotation (e.g., considering both “DC_cluster1” and “DC_cluster2” as DC cells). For cross-validation benchmarks, we performed the classification using the function scmapCluster of scmap without considering the unassigned cells.
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