Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Bacterial and virus strains | ||
| Biological samples | ||
| Whole slide images (TCGA) | https://portal.gdc.cancer.gov/ | RRID:SCR_003193 |
| Chemicals, peptides, and recombinant proteins | ||
| Critical commercial assays | ||
| Deposited data | ||
| The Cancer Genome Atlas | https://portal.gdc.cancer.gov/ | RRID:SCR_003193 |
| Experimental models: Cell lines | ||
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and algorithms | ||
| PORPOISE | This paper; https://github.com/mahmoodlab/PORPOISE | |
| CLAM | https://github.com/mahmoodlab/CLAM | |
| Pathomic Fusion | https://github.com/mahmoodlab/PathomicFusion | |
| HoVeR-Net | https://github.com/vqdang/hover_net | |
| Python (3.7.7) | https://www.python.org/ | RRID:SCR_008394 |
| NVIDIA CUDA (11.0) | https://developer.nvidia.com/cuda-toolkit | |
| NVIDIA cuDNN (7.5) | https://developer.nvidia.com/cudnn | |
| PyTorch (1.6.0) | https://pytorch.org | RRID:SCR_018536 |
| Captum (0.2.0) | https://captum.ai | |
| NumPy (1.18.1) | http://www.numpy.org | RRID:SCR_008633 |
| Pandas (1.1.3) | https://pandas.pydata.org | RRID:SCR_018214 |
| PIL (7.0.0) | https://pillow.readthedocs.io/en/stable/ | |
| Openslide (1.1.1) | https://openslide.org/ | |
| Scipy (1.4.1) | http://www.scipy.org | RRID:SCR_008058 |
| Lifelines (0.24.6) | https://lifelines.readthedocs.io/ | |
| Seaborn (0.9.0) | https://seaborn.pydata.org/ | |
| Matplotlib (3.1.1) | https://matplotlib.org/ | RRID:SCR_008624 |
| Shap (0.35.0) | https://shap.readthedocs.io/en/latest/index.html | |
| Other | ||