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Benchmarking Starfysh against other methods on the simulated dataset: Pearson correlation of ground truth and estimated proportions per cell type in data. The performance of each method is summarized by computing the average root-mean-squared error (RMSE) across spots against the ground truth ( Methods ). Additional benchmarking and robustness analysis results are shown in Supplementary Fig. 2c–e . Benchmarking on real breast tumor ST data is shown in Supplementary Fig. 3a–d ( Methods ). corr., correlation; ref-free, reference free; sc-ref, reference with scRNA-seq data.

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