├── .gitignore ├── LICENSE.md ├── README.md ├── attention_map.py ├── attention_map_fp.py ├── attention_score.py ├── color_normalization ├── 44286 │ └── wc_snmf_06.npy └── ref │ ├── merge_tiles_lab_mean.npy │ ├── merge_tiles_lab_std.npy │ └── wc_pca.npy ├── create_patches.py ├── create_patches_fp.py ├── create_splits_seq.py ├── data └── bgr_intensity_tcga.csv ├── data_augm.py ├── dataset_csv ├── tcga_hcc_349_Inflammatory_highvsrest.csv └── tcga_hcc_feature_349.csv ├── datasets ├── dataset_generic.py └── dataset_h5.py ├── docs ├── clam.yml ├── deepai.yml ├── dirty_stitched_A95S.jpg ├── incomplete_mask_AAVV.png ├── seg_A9H4.png ├── seg_anno_A9H4.jpg ├── vis.png └── workflow.png ├── eval.py ├── eval_customed_models.py ├── eval_customed_models_fp.py ├── eval_customed_models_slide_aggregation.py ├── extract_features.py ├── extract_features_fp.py ├── gene_clust ├── codes │ ├── PlotHeatmapGeneSignature.R │ ├── tcga_clustering.ipynb │ ├── tcga_fpkm_processing.ipynb │ └── tcga_label_csv_for_clam.ipynb ├── data │ ├── IDsTCGA.xlsx │ ├── ProbeAnnotations_NS_IO_360_v1.0_clean.csv │ ├── TCGA_HCC_no_gene_expression.csv │ ├── TCGA_HCC_no_slide.csv │ ├── TCGA_samples.csv │ └── fpkm_TCGA_CCL3L1.csv └── results │ ├── tcga │ ├── clustermap_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── clustermap_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── clustermap_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── clustermap_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf │ ├── fpkm_final_add1-log2-zscore_336.csv │ ├── fpkm_final_raw_CCL3L1_336.csv │ ├── sample_clusters_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv │ ├── sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv │ ├── sample_clusters_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv │ ├── sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_3_reorder.csv │ ├── sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv │ └── sample_clusters_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_3_reorder.csv │ └── tcga_python │ ├── clustermap_6G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf │ ├── clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf │ ├── clustermap_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf │ ├── clustermap_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_2_3.pdf │ ├── clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf │ ├── clustermap_T-cell_Exhaustion_zscore_hc_ward_euclidean_2_3.pdf │ ├── sample_clusters_6G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv │ ├── sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_3.csv │ ├── sample_clusters_Inflammatory_zscore_hc_ward_euclidean_3.csv │ ├── sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_3.csv │ ├── sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv │ └── sample_clusters_T-cell_Exhaustion_zscore_hc_ward_euclidean_3.csv ├── main.py ├── models ├── model_clam.py ├── model_mil.py └── resnet_custom.py ├── results ├── patches-fp_examples │ ├── TCGA-2V-A95S-01Z-00-DX1.9DFA6FC7-87A6-4C14-9A39-E3F12B01C4D4.h5 │ ├── TCGA-2Y-A9GS-01Z-00-DX1.75C5CEF1-6C8B-42FF-82F6-9A05621E9A80.h5 │ ├── TCGA-2Y-A9GT-01Z-00-DX1.30666775-3556-4DFE-A5EC-8CCF8EEB1803.h5 │ ├── TCGA-2Y-A9GU-01Z-00-DX1.700CBBD7-9F58-470D-A85B-C7BAE5608018.h5 │ ├── TCGA-2Y-A9GV-01Z-00-DX1.524FA6DD-7C84-425C-A2B5-17690DF50A28.h5 │ ├── TCGA-2Y-A9GW-01Z-00-DX1.71805205-933D-4D72-A4A2-586DC5490D76.h5 │ ├── TCGA-2Y-A9GX-01Z-00-DX1.DC3E1EAB-686A-44F9-91AF-0C6975DE029E.h5 │ ├── TCGA-2Y-A9GY-01Z-00-DX1.9AF8DAB8-B99C-4484-A065-20E7345E1FF4.h5 │ ├── TCGA-2Y-A9GZ-01Z-00-DX1.4E8C9A7D-D21D-4B6E-8C1B-DC520309AB91.h5 │ ├── TCGA-2Y-A9H0-01Z-00-DX1.E1725D1E-B135-47B3-820B-BEE1FC4EDCF0.h5 │ ├── TCGA-2Y-A9H1-01Z-00-DX1.FE4D124E-AB92-4083-8D09-F025B0C637EB.h5 │ ├── TCGA-2Y-A9H2-01Z-00-DX1.D1B4968D-8AAD-4F12-8447-6FC752E8DDE4.h5 │ ├── TCGA-2Y-A9H3-01Z-00-DX1.813C14D8-DBBC-43AF-9E3A-9EFC1D1AFC98.h5 │ ├── TCGA-2Y-A9H4-01Z-00-DX1.897C9E71-7FD7-4229-9A95-F61AE43D0FDA.h5 │ └── TCGA-2Y-A9H5-01Z-00-DX1.08348C3C-A16F-45F6-8AE9-D0613268D703.h5 ├── process_list_edited_20x.csv └── process_list_edited_40x.csv ├── splits ├── camelyon_40x_cv_50 │ ├── splits_0.csv │ ├── splits_0_bool.csv │ ├── splits_0_descriptor.csv │ ├── splits_1.csv │ ├── splits_1_bool.csv │ ├── splits_1_descriptor.csv │ ├── splits_2.csv │ ├── splits_2_bool.csv │ ├── splits_2_descriptor.csv │ ├── splits_3.csv │ ├── splits_3_bool.csv │ ├── splits_3_descriptor.csv │ ├── splits_4.csv │ ├── splits_4_bool.csv │ ├── splits_4_descriptor.csv │ ├── splits_5.csv │ ├── splits_5_bool.csv │ ├── splits_5_descriptor.csv │ ├── splits_6.csv │ ├── splits_6_bool.csv │ ├── splits_6_descriptor.csv │ ├── splits_7.csv │ ├── splits_7_bool.csv │ ├── splits_7_descriptor.csv │ ├── splits_8.csv │ ├── splits_8_bool.csv │ ├── splits_8_descriptor.csv │ ├── splits_9.csv │ ├── splits_9_bool.csv │ └── splits_9_descriptor.csv ├── camelyon_40x_cv_75 │ ├── splits_0.csv │ ├── splits_0_bool.csv │ ├── splits_0_descriptor.csv │ ├── splits_1.csv │ ├── splits_1_bool.csv │ ├── splits_1_descriptor.csv │ ├── splits_2.csv │ ├── splits_2_bool.csv │ ├── splits_2_descriptor.csv │ ├── splits_3.csv │ ├── splits_3_bool.csv │ ├── splits_3_descriptor.csv │ ├── splits_4.csv │ ├── splits_4_bool.csv │ ├── splits_4_descriptor.csv │ ├── splits_5.csv │ ├── splits_5_bool.csv │ ├── splits_5_descriptor.csv │ ├── splits_6.csv │ ├── splits_6_bool.csv │ ├── splits_6_descriptor.csv │ ├── splits_7.csv │ ├── splits_7_bool.csv │ ├── splits_7_descriptor.csv │ ├── splits_8.csv │ ├── splits_8_bool.csv │ ├── splits_8_descriptor.csv │ ├── splits_9.csv │ ├── splits_9_bool.csv │ └── splits_9_descriptor.csv ├── tcga_hcc_349_Inflammatory_cv_highvsrest_622_100 │ ├── splits_0.csv │ ├── splits_0_bool.csv │ ├── splits_0_descriptor.csv │ ├── splits_1.csv │ ├── splits_1_bool.csv │ ├── splits_1_descriptor.csv │ ├── splits_2.csv │ ├── splits_2_bool.csv │ ├── splits_2_descriptor.csv │ ├── splits_3.csv │ ├── splits_3_bool.csv │ ├── splits_3_descriptor.csv │ ├── splits_4.csv │ ├── splits_4_bool.csv │ ├── splits_4_descriptor.csv │ ├── splits_5.csv │ ├── splits_5_bool.csv │ ├── splits_5_descriptor.csv │ ├── splits_6.csv │ ├── splits_6_bool.csv │ ├── splits_6_descriptor.csv │ ├── splits_7.csv │ ├── splits_7_bool.csv │ ├── splits_7_descriptor.csv │ ├── splits_8.csv │ ├── splits_8_bool.csv │ ├── splits_8_descriptor.csv │ ├── splits_9.csv │ ├── splits_9_bool.csv │ └── splits_9_descriptor.csv └── tcga_kidney_cv_50 │ ├── splits_0.csv │ ├── splits_0_bool.csv │ ├── splits_0_descriptor.csv │ ├── splits_1.csv │ ├── splits_1_bool.csv │ ├── splits_1_descriptor.csv │ ├── splits_2.csv │ ├── splits_2_bool.csv │ ├── splits_2_descriptor.csv │ ├── splits_3.csv │ ├── splits_3_bool.csv │ ├── splits_3_descriptor.csv │ ├── splits_4.csv │ ├── splits_4_bool.csv │ ├── splits_4_descriptor.csv │ ├── splits_5.csv │ ├── splits_5_bool.csv │ ├── splits_5_descriptor.csv │ ├── splits_6.csv │ ├── splits_6_bool.csv │ ├── splits_6_descriptor.csv │ ├── splits_7.csv │ ├── splits_7_bool.csv │ ├── splits_7_descriptor.csv │ ├── splits_8.csv │ ├── splits_8_bool.csv │ ├── splits_8_descriptor.csv │ ├── splits_9.csv │ ├── splits_9_bool.csv │ └── splits_9_descriptor.csv ├── stitch_tumor.py ├── train_customed_models.py ├── train_customed_models_fp.py ├── tutorials ├── clam.md ├── clam_anno.md ├── clam_fp.md ├── clam_fp_anno.md ├── external_validation.md ├── install_clam.md ├── mil.md ├── mil_anno.md ├── mil_fp.md ├── mil_fp_anno.md ├── other_settings.md ├── patch-based.md ├── patch-based_anno.md ├── patch-based_fp.md └── patch-based_fp_anno.md ├── utils ├── core_utils.py ├── eval_utils.py ├── file_utils.py └── utils.py └── wsi_core ├── WholeSlideImage.py └── wsi_utils.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pt 2 | **/.DS_Store 3 | __pycache__/ -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/README.md -------------------------------------------------------------------------------- /attention_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/attention_map.py -------------------------------------------------------------------------------- /attention_map_fp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/attention_map_fp.py -------------------------------------------------------------------------------- /attention_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/attention_score.py -------------------------------------------------------------------------------- /color_normalization/44286/wc_snmf_06.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/color_normalization/44286/wc_snmf_06.npy -------------------------------------------------------------------------------- /color_normalization/ref/merge_tiles_lab_mean.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/color_normalization/ref/merge_tiles_lab_mean.npy -------------------------------------------------------------------------------- /color_normalization/ref/merge_tiles_lab_std.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/color_normalization/ref/merge_tiles_lab_std.npy -------------------------------------------------------------------------------- /color_normalization/ref/wc_pca.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/color_normalization/ref/wc_pca.npy -------------------------------------------------------------------------------- /create_patches.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/create_patches.py -------------------------------------------------------------------------------- /create_patches_fp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/create_patches_fp.py -------------------------------------------------------------------------------- /create_splits_seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/create_splits_seq.py -------------------------------------------------------------------------------- /data/bgr_intensity_tcga.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/data/bgr_intensity_tcga.csv -------------------------------------------------------------------------------- /data_augm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/data_augm.py -------------------------------------------------------------------------------- /dataset_csv/tcga_hcc_349_Inflammatory_highvsrest.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/dataset_csv/tcga_hcc_349_Inflammatory_highvsrest.csv -------------------------------------------------------------------------------- /dataset_csv/tcga_hcc_feature_349.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/dataset_csv/tcga_hcc_feature_349.csv -------------------------------------------------------------------------------- /datasets/dataset_generic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/datasets/dataset_generic.py -------------------------------------------------------------------------------- /datasets/dataset_h5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/datasets/dataset_h5.py -------------------------------------------------------------------------------- /docs/clam.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/clam.yml -------------------------------------------------------------------------------- /docs/deepai.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/deepai.yml -------------------------------------------------------------------------------- /docs/dirty_stitched_A95S.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/dirty_stitched_A95S.jpg -------------------------------------------------------------------------------- /docs/incomplete_mask_AAVV.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/incomplete_mask_AAVV.png -------------------------------------------------------------------------------- /docs/seg_A9H4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/seg_A9H4.png -------------------------------------------------------------------------------- /docs/seg_anno_A9H4.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/seg_anno_A9H4.jpg -------------------------------------------------------------------------------- /docs/vis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/vis.png -------------------------------------------------------------------------------- /docs/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/docs/workflow.png -------------------------------------------------------------------------------- /eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/eval.py -------------------------------------------------------------------------------- /eval_customed_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/eval_customed_models.py -------------------------------------------------------------------------------- /eval_customed_models_fp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/eval_customed_models_fp.py -------------------------------------------------------------------------------- /eval_customed_models_slide_aggregation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/eval_customed_models_slide_aggregation.py -------------------------------------------------------------------------------- /extract_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/extract_features.py -------------------------------------------------------------------------------- /extract_features_fp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/extract_features_fp.py -------------------------------------------------------------------------------- /gene_clust/codes/PlotHeatmapGeneSignature.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/codes/PlotHeatmapGeneSignature.R -------------------------------------------------------------------------------- /gene_clust/codes/tcga_clustering.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/codes/tcga_clustering.ipynb -------------------------------------------------------------------------------- /gene_clust/codes/tcga_fpkm_processing.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/codes/tcga_fpkm_processing.ipynb -------------------------------------------------------------------------------- /gene_clust/codes/tcga_label_csv_for_clam.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/codes/tcga_label_csv_for_clam.ipynb -------------------------------------------------------------------------------- /gene_clust/data/IDsTCGA.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/IDsTCGA.xlsx -------------------------------------------------------------------------------- /gene_clust/data/ProbeAnnotations_NS_IO_360_v1.0_clean.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/ProbeAnnotations_NS_IO_360_v1.0_clean.csv -------------------------------------------------------------------------------- /gene_clust/data/TCGA_HCC_no_gene_expression.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/TCGA_HCC_no_gene_expression.csv -------------------------------------------------------------------------------- /gene_clust/data/TCGA_HCC_no_slide.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/TCGA_HCC_no_slide.csv -------------------------------------------------------------------------------- /gene_clust/data/TCGA_samples.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/TCGA_samples.csv -------------------------------------------------------------------------------- /gene_clust/data/fpkm_TCGA_CCL3L1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/data/fpkm_TCGA_CCL3L1.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_Inflammatory_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/clustermap_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/clustermap_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_2_3_reorder.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga/fpkm_final_add1-log2-zscore_336.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/fpkm_final_add1-log2-zscore_336.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/fpkm_final_raw_CCL3L1_336.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/fpkm_final_raw_CCL3L1_336.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_6G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_Inflammatory_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga/sample_clusters_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_3_reorder.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga/sample_clusters_T-cell_Exhaustion_zscore_hc_ward.D2_euclidean_3_reorder.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_6G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_6G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_Inflammatory_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/clustermap_T-cell_Exhaustion_zscore_hc_ward_euclidean_2_3.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/clustermap_T-cell_Exhaustion_zscore_hc_ward_euclidean_2_3.pdf -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_6G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_6G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_Gajewski_13G_Inflammatory_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_Inflammatory_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_Inflammatory_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_Interferon_Gamma_Biology_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_Ribas_10G_Interferon_Gamma_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /gene_clust/results/tcga_python/sample_clusters_T-cell_Exhaustion_zscore_hc_ward_euclidean_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/gene_clust/results/tcga_python/sample_clusters_T-cell_Exhaustion_zscore_hc_ward_euclidean_3.csv -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/main.py -------------------------------------------------------------------------------- /models/model_clam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/models/model_clam.py -------------------------------------------------------------------------------- /models/model_mil.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/models/model_mil.py -------------------------------------------------------------------------------- /models/resnet_custom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/models/resnet_custom.py -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2V-A95S-01Z-00-DX1.9DFA6FC7-87A6-4C14-9A39-E3F12B01C4D4.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2V-A95S-01Z-00-DX1.9DFA6FC7-87A6-4C14-9A39-E3F12B01C4D4.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GS-01Z-00-DX1.75C5CEF1-6C8B-42FF-82F6-9A05621E9A80.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GS-01Z-00-DX1.75C5CEF1-6C8B-42FF-82F6-9A05621E9A80.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GT-01Z-00-DX1.30666775-3556-4DFE-A5EC-8CCF8EEB1803.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GT-01Z-00-DX1.30666775-3556-4DFE-A5EC-8CCF8EEB1803.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GU-01Z-00-DX1.700CBBD7-9F58-470D-A85B-C7BAE5608018.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GU-01Z-00-DX1.700CBBD7-9F58-470D-A85B-C7BAE5608018.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GV-01Z-00-DX1.524FA6DD-7C84-425C-A2B5-17690DF50A28.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GV-01Z-00-DX1.524FA6DD-7C84-425C-A2B5-17690DF50A28.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GW-01Z-00-DX1.71805205-933D-4D72-A4A2-586DC5490D76.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GW-01Z-00-DX1.71805205-933D-4D72-A4A2-586DC5490D76.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GX-01Z-00-DX1.DC3E1EAB-686A-44F9-91AF-0C6975DE029E.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GX-01Z-00-DX1.DC3E1EAB-686A-44F9-91AF-0C6975DE029E.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GY-01Z-00-DX1.9AF8DAB8-B99C-4484-A065-20E7345E1FF4.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GY-01Z-00-DX1.9AF8DAB8-B99C-4484-A065-20E7345E1FF4.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9GZ-01Z-00-DX1.4E8C9A7D-D21D-4B6E-8C1B-DC520309AB91.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9GZ-01Z-00-DX1.4E8C9A7D-D21D-4B6E-8C1B-DC520309AB91.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H0-01Z-00-DX1.E1725D1E-B135-47B3-820B-BEE1FC4EDCF0.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H0-01Z-00-DX1.E1725D1E-B135-47B3-820B-BEE1FC4EDCF0.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H1-01Z-00-DX1.FE4D124E-AB92-4083-8D09-F025B0C637EB.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H1-01Z-00-DX1.FE4D124E-AB92-4083-8D09-F025B0C637EB.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H2-01Z-00-DX1.D1B4968D-8AAD-4F12-8447-6FC752E8DDE4.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H2-01Z-00-DX1.D1B4968D-8AAD-4F12-8447-6FC752E8DDE4.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H3-01Z-00-DX1.813C14D8-DBBC-43AF-9E3A-9EFC1D1AFC98.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H3-01Z-00-DX1.813C14D8-DBBC-43AF-9E3A-9EFC1D1AFC98.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H4-01Z-00-DX1.897C9E71-7FD7-4229-9A95-F61AE43D0FDA.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H4-01Z-00-DX1.897C9E71-7FD7-4229-9A95-F61AE43D0FDA.h5 -------------------------------------------------------------------------------- /results/patches-fp_examples/TCGA-2Y-A9H5-01Z-00-DX1.08348C3C-A16F-45F6-8AE9-D0613268D703.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/patches-fp_examples/TCGA-2Y-A9H5-01Z-00-DX1.08348C3C-A16F-45F6-8AE9-D0613268D703.h5 -------------------------------------------------------------------------------- /results/process_list_edited_20x.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/process_list_edited_20x.csv -------------------------------------------------------------------------------- /results/process_list_edited_40x.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/results/process_list_edited_40x.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_0.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_0.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_0_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_0_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_0_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_0_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_1.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_1_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_1_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_1_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_1_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_2.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_2_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_2_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_2_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_2_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_3.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_3_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_3_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_3_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_3_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_4.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_4_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_4_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_4_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_4_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_5.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_5_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_5_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_5_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_5_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_6.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_6.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_6_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_6_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_6_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_6_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_7.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_7.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_7_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_7_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_7_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_7_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_8.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_8.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_8_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_8_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_8_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_8_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_9.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_9.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_9_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_9_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_50/splits_9_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_50/splits_9_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_0.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_0.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_0_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_0_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_0_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_0_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_1.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_1_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_1_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_1_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_1_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_2.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_2_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_2_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_2_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_2_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_3.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_3_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_3_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_3_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_3_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_4.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_4_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_4_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_4_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_4_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_5.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_5_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_5_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_5_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_5_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_6.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_6.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_6_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_6_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_6_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_6_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_7.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_7.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_7_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_7_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_7_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_7_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_8.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_8.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_8_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_8_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_8_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_8_descriptor.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_9.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_9.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_9_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_9_bool.csv -------------------------------------------------------------------------------- /splits/camelyon_40x_cv_75/splits_9_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/camelyon_40x_cv_75/splits_9_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_0_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_1_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_2_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_3_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_4_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_5_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_6_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_7_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_8_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9_bool.csv -------------------------------------------------------------------------------- /splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_hcc_349_Inflammatory_cv_highvsrest_622_100/splits_9_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_0.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_0.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_0_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_0_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_0_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_0_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_1.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_1_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_1_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_1_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_1_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_2.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_2_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_2_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_2_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_2_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_3.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_3_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_3_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_3_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_3_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_4.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_4.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_4_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_4_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_4_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_4_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_5.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_5.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_5_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_5_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_5_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_5_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_6.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_6.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_6_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_6_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_6_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_6_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_7.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_7.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_7_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_7_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_7_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_7_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_8.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_8.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_8_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_8_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_8_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_8_descriptor.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_9.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_9.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_9_bool.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_9_bool.csv -------------------------------------------------------------------------------- /splits/tcga_kidney_cv_50/splits_9_descriptor.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/splits/tcga_kidney_cv_50/splits_9_descriptor.csv -------------------------------------------------------------------------------- /stitch_tumor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/stitch_tumor.py -------------------------------------------------------------------------------- /train_customed_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/train_customed_models.py -------------------------------------------------------------------------------- /train_customed_models_fp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/train_customed_models_fp.py -------------------------------------------------------------------------------- /tutorials/clam.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/clam.md -------------------------------------------------------------------------------- /tutorials/clam_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/clam_anno.md -------------------------------------------------------------------------------- /tutorials/clam_fp.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/clam_fp.md -------------------------------------------------------------------------------- /tutorials/clam_fp_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/clam_fp_anno.md -------------------------------------------------------------------------------- /tutorials/external_validation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/external_validation.md -------------------------------------------------------------------------------- /tutorials/install_clam.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/install_clam.md -------------------------------------------------------------------------------- /tutorials/mil.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/mil.md -------------------------------------------------------------------------------- /tutorials/mil_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/mil_anno.md -------------------------------------------------------------------------------- /tutorials/mil_fp.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/mil_fp.md -------------------------------------------------------------------------------- /tutorials/mil_fp_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/mil_fp_anno.md -------------------------------------------------------------------------------- /tutorials/other_settings.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/other_settings.md -------------------------------------------------------------------------------- /tutorials/patch-based.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/patch-based.md -------------------------------------------------------------------------------- /tutorials/patch-based_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/patch-based_anno.md -------------------------------------------------------------------------------- /tutorials/patch-based_fp.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/patch-based_fp.md -------------------------------------------------------------------------------- /tutorials/patch-based_fp_anno.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/tutorials/patch-based_fp_anno.md -------------------------------------------------------------------------------- /utils/core_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/utils/core_utils.py -------------------------------------------------------------------------------- /utils/eval_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/utils/eval_utils.py -------------------------------------------------------------------------------- /utils/file_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/utils/file_utils.py -------------------------------------------------------------------------------- /utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/utils/utils.py -------------------------------------------------------------------------------- /wsi_core/WholeSlideImage.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/wsi_core/WholeSlideImage.py -------------------------------------------------------------------------------- /wsi_core/wsi_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qinghezeng/Histo2GeneSignatures/HEAD/wsi_core/wsi_utils.py --------------------------------------------------------------------------------