The CytoTRACE algorithm is an unsupervised framework used to predict relative differentiation states from single-cell transcriptomes21. It has been validated in large-scale datasets and has shown superior performance compared to existing computational techniques for assessing stemness. The CytoTRACE algorithm calculates the gene expression matrix and assigns a score to each individual cell, representing its stemness. In this study, we utilized the R package CytoTRACE to calculate the CytoTRACE score specifically for malignant cells. The ScanoramaCT python module was exploited to mitigate batch effects within the datasets. The CytoTRACE scores range from 0 to 1, with higher scores indicating higher stemness (lower differentiation) and vice versa.
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