Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model

This dataset contains the processed scRNA-seq data and code for single-cell unified polarization assessment. Please refer to the article "Scupa: Single-cell unified polarization assessment of immune cells using the single-cell foundation model" for the detailed data and method description.

*.rds: the processed scRNA-seq datasets with Universal Cell Embeddings saved as a Seurat object. The Universal Cell Embeddings are saved in the assay 'uce'.

immune_dict_uce.rds: Immune Dictionary.

ifnb_treatment_uce.rds: human PBMCs treated with IFN-beta.

macrophage_stimulation_uce.rds: human macrophages treated with one or two of IFN-beta, IFN-gamma, TNF-alpha and IL-4.

il2_treatment_uce.rds: mouse spleen CD8+ T cells treated with IL-2 or anti-PD-L1.

pan_cancer_myeloid_uce.rds: tumor-infiltrating myeloid cells across seven cancer types.

notebooks.zip: Jupyter notebooks containing code for training models and applications to multiple datasets.