AURORAData/AURORA_prediction

AURORA (Architecture Unveiling through RNA Omics and Routine Histology Analysis)

• trained_models: Pretrained AURORA models for LUAD, KIRC and BRCA.

  • *.pth: model weight;
  • *.json: parameters for the AURORA model;
  • *.csv: supporting information (cell types, gene names and normalizing factors) used by *.json.

• predictions_112um: Virtual spatial transcriptomics at 112 μm * 112 μm by AURORA of TCGA-LUAD, TCGA-KIRC, TCGA-BRCA and BRCA pre-chemotherapy (https://doi.org/10.1038/s41586-021-04278-5) samples.

  • *.h5 file: virtual spatial transcriptomics
    • pos: spatial coordinates of patches (224 pixels * 224 pixels). This is the coordinates of the upper left corner of each patch.
    • gene_exp: gene expressions. The names of the genes are stored in genes.csv.
    • celltype_prop: cell type proportions in log scales. The name of the cell types are stored in celltypes.csv.
  • genes.csv: names of predicted genes.
  • celltypes.csv: names of predicted cell types.