| --- |
| license: other |
| license_name: penn-license |
| license_link: LICENSE |
| viewer: false |
| tags: |
| - SpatialTranscriptomics |
| - VirtualPrediction |
| --- |
| **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. |
