├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── config ├── __init__.py ├── ct_default.yaml ├── data │ ├── data.yaml │ ├── data_histogene.yaml │ ├── data_istar.yaml │ ├── data_mclstexp.yaml │ ├── data_simulation.yaml │ ├── data_test.yaml │ └── data_thitogene.yaml ├── gene_default.yaml ├── gene_histogene.yaml ├── gene_istar.yaml ├── gene_mclstexp.yaml ├── gene_simulation.yaml ├── gene_test.yaml ├── gene_thitogene.yaml ├── model │ └── model.yaml ├── predictor │ └── gene_predictor.yaml └── trainer │ ├── trainer.yaml │ └── trainer_test.yaml ├── data ├── .gitkeep ├── HEST_v1_1_0.csv ├── genes_1000_hvg_sim.csv ├── genes_Kidney_500_hvg_bench.csv ├── genes_Kidney_500_svg_bench.csv ├── genes_Kidney_50_hvg_bench.csv ├── genes_Kidney_50_svg_bench.csv ├── genes_Prostate_500_hvg_bench.csv ├── genes_Prostate_500_svg_bench.csv ├── genes_Prostate_50_hvg_bench.csv ├── genes_Prostate_50_svg_bench.csv ├── genes_marker_ovary.csv ├── genes_marker_sim.csv ├── genes_xenium_Breast.csv └── imagenet_stats.json ├── environment.yml ├── external ├── HisToGene │ ├── LICENSE │ ├── README.md │ ├── Workflow.PNG │ ├── data │ │ ├── download.sh │ │ └── her_hvg_cut_1000.npy │ ├── dataset.py │ ├── model │ │ └── download_checkpoint.txt │ ├── predict.py │ ├── transformer.py │ ├── tutorial.ipynb │ ├── utils.py │ └── vis_model.py ├── THItoGene │ ├── GATLayer.py │ ├── ODConv.py │ ├── README.md │ ├── THItoGene.yml │ ├── data │ │ ├── download.sh │ │ ├── her_hvg_cut_1000.npy │ │ └── skin_hvg_cut_1000.npy │ ├── dataset.py │ ├── efficient_capsnet.py │ ├── graph_construction.py │ ├── model │ │ └── download.txt │ ├── predict.py │ ├── requirements.txt │ ├── train.py │ ├── transformer.py │ ├── utils.py │ ├── vis_model.py │ └── workflow.png ├── cell_SSL │ ├── CODE_OF_CONDUCT.md │ ├── CONFIG.md │ ├── CONTRIBUTING.md │ ├── LICENSE │ ├── README.md │ ├── __init__.py │ ├── augmentations.py │ ├── convert_to_deit.py │ ├── data_utils.py │ ├── dataset_utils.py │ ├── main_lincls.py │ ├── main_moco.py │ ├── moco │ │ ├── __init__.py │ │ ├── builder.py │ │ ├── loader.py │ │ └── optimizer.py │ ├── poetry.lock │ ├── pyproject.toml │ ├── transfer │ │ ├── README.md │ │ ├── __init__.py │ │ ├── datasets.py │ │ ├── oxford_flowers_dataset.py │ │ └── oxford_pets_dataset.py │ └── vits.py ├── istar │ ├── LICENSE │ ├── README.md │ ├── aggregate_imputed.py │ ├── cluster.py │ ├── connected_components.py │ ├── data │ │ └── markers │ │ │ ├── cell-type-template.tsv │ │ │ └── signature-score-template.txt │ ├── differential.py │ ├── download_checkpoints.sh │ ├── download_demo.sh │ ├── enrich.py │ ├── extract_features.py │ ├── get_mask.py │ ├── hipt_4k.py │ ├── hipt_heatmap_utils.py │ ├── hipt_model_utils.py │ ├── image.py │ ├── impute.py │ ├── impute_by_basic.py │ ├── marker_score.py │ ├── pixannot.py │ ├── plot_imputed.py │ ├── plot_spots.py │ ├── preprocess.py │ ├── reduce_dim.py │ ├── reorganize_imputed.py │ ├── requirements.txt │ ├── rescale.py │ ├── run.sh │ ├── run_demo.sh │ ├── select_genes.py │ ├── structural_similarity.py │ ├── train.py │ ├── utils.py │ ├── vision_transformer.py │ ├── vision_transformer4k.py │ └── visual.py └── mclSTExp │ ├── README.md │ ├── baselines │ ├── Bleep │ │ ├── BLEEP_inference.ipynb │ │ ├── BLEEP_main.py │ │ ├── BLEEP_overview.png │ │ ├── LICENSE │ │ ├── config.py │ │ ├── dataset.py │ │ ├── models.py │ │ ├── modules.py │ │ ├── preprocess.ipynb │ │ └── utils.py │ ├── His2ST │ │ ├── HIST2ST.py │ │ ├── HIST2ST_train.py │ │ ├── NB_module.py │ │ ├── Workflow.png │ │ ├── dataset.py │ │ ├── gcn.py │ │ ├── graph_construction.py │ │ ├── predict.py │ │ ├── run_trained_models.ipynb │ │ ├── transformer.py │ │ ├── tutorial.ipynb │ │ └── utils.py │ ├── HisToGene │ │ ├── LICENSE │ │ ├── Workflow.PNG │ │ ├── dataset.py │ │ ├── predict.py │ │ ├── transformer.py │ │ ├── tutorial.ipynb │ │ ├── utils.py │ │ └── vis_model.py │ ├── ReadMe │ └── THItoGene │ │ ├── GATLayer.py │ │ ├── ODConv.py │ │ ├── THItoGene.yml │ │ ├── dataset.py │ │ ├── efficient_capsnet.py │ │ ├── graph_construction.py │ │ ├── predict.py │ │ ├── requirements.txt │ │ ├── train.py │ │ ├── transformer.py │ │ ├── utils │ │ ├── vis_model.py │ │ └── workflow.png │ ├── data │ ├── 1000hvg_common.pkl │ ├── download.sh │ ├── her_hvg_cut_1000.npy │ └── skin_hvg_cut_1000.npy │ ├── dataset.py │ ├── evel_cscc.py │ ├── evel_her2st.py │ ├── evel_visium.py │ ├── hvg_cscc.py │ ├── hvg_her2st.py │ ├── hvg_visium.py │ ├── model.py │ ├── train.py │ ├── tutorial.ipynb │ ├── utils.py │ └── workflow.png ├── full_pipeline_script.py ├── method.jpg ├── scellst ├── __init__.py ├── bench │ ├── __init__.py │ ├── bench_data_handler.py │ ├── bench_dataset.py │ ├── data_formatting.py │ ├── utils_data.py │ ├── utils_histogene.py │ ├── utils_istar.py │ ├── utils_mclstexp.py │ └── utils_thitogene.py ├── cellhest_adapter │ ├── __init__.py │ ├── aggregation.py │ ├── cell_hest_data.py │ ├── cell_utils.py │ ├── data_mixin.py │ ├── h5_utils.py │ ├── plot_mixin.py │ └── processing_utils.py ├── constant.py ├── dataset │ ├── __init__.py │ ├── batch_sampler.py │ ├── cell_image_dataset.py │ ├── data_handler.py │ ├── data_module.py │ ├── dataset_utils.py │ ├── gene_utils.py │ └── torch_dataset.py ├── lightning_model │ ├── __init__.py │ ├── base_lightning_model.py │ └── gene_lightning_model.py ├── metrics │ ├── __init__.py │ ├── gene.py │ └── metric_utils.py ├── model │ ├── __init__.py │ ├── base_mil_model.py │ ├── instance_mil_distribution.py │ └── instance_mil_model.py ├── module │ ├── __init__.py │ ├── distributions.py │ ├── gene_predictor.py │ └── image_encoder.py ├── plots │ ├── __init__.py │ ├── plot_hest.py │ ├── plot_metrics.py │ ├── plot_spatial.py │ └── plot_ssl.py ├── predict.py ├── submit_function.py ├── train.py ├── trainer.py ├── type.py └── utils │ ├── __init__.py │ ├── img_utils.py │ ├── io_utils.py │ └── utils.py ├── simulation ├── __init__.py ├── data_loader.py ├── data_preparation.py ├── decoupler_utils.py ├── main.py ├── sim_data_utils.py ├── supervised_lightning_model.py └── supervised_model.py └── training_tutorial.ipynb /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/.gitmodules -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/README.md -------------------------------------------------------------------------------- /config/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config/ct_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/ct_default.yaml -------------------------------------------------------------------------------- /config/data/data.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data.yaml -------------------------------------------------------------------------------- /config/data/data_histogene.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_histogene.yaml -------------------------------------------------------------------------------- /config/data/data_istar.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_istar.yaml -------------------------------------------------------------------------------- /config/data/data_mclstexp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_mclstexp.yaml -------------------------------------------------------------------------------- /config/data/data_simulation.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_simulation.yaml -------------------------------------------------------------------------------- /config/data/data_test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_test.yaml -------------------------------------------------------------------------------- /config/data/data_thitogene.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/data/data_thitogene.yaml -------------------------------------------------------------------------------- /config/gene_default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_default.yaml -------------------------------------------------------------------------------- /config/gene_histogene.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_histogene.yaml -------------------------------------------------------------------------------- /config/gene_istar.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_istar.yaml -------------------------------------------------------------------------------- /config/gene_mclstexp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_mclstexp.yaml -------------------------------------------------------------------------------- /config/gene_simulation.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_simulation.yaml -------------------------------------------------------------------------------- /config/gene_test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_test.yaml -------------------------------------------------------------------------------- /config/gene_thitogene.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/gene_thitogene.yaml -------------------------------------------------------------------------------- /config/model/model.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/model/model.yaml -------------------------------------------------------------------------------- /config/predictor/gene_predictor.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/config/predictor/gene_predictor.yaml -------------------------------------------------------------------------------- /config/trainer/trainer.yaml: -------------------------------------------------------------------------------- 1 | trainer: 2 | patience: 20 3 | max_epoch: 400 4 | -------------------------------------------------------------------------------- /config/trainer/trainer_test.yaml: -------------------------------------------------------------------------------- 1 | trainer: 2 | patience: 20 3 | max_epoch: 5 4 | -------------------------------------------------------------------------------- /data/.gitkeep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/HEST_v1_1_0.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/data/HEST_v1_1_0.csv -------------------------------------------------------------------------------- /data/genes_1000_hvg_sim.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Kidney_500_hvg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Kidney_500_svg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Kidney_50_hvg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Kidney_50_svg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Prostate_500_hvg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Prostate_500_svg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Prostate_50_hvg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_Prostate_50_svg_bench.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_marker_ovary.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/data/genes_marker_ovary.csv -------------------------------------------------------------------------------- /data/genes_marker_sim.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/genes_xenium_Breast.csv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /data/imagenet_stats.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/data/imagenet_stats.json -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/environment.yml -------------------------------------------------------------------------------- /external/HisToGene/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/LICENSE -------------------------------------------------------------------------------- /external/HisToGene/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/README.md -------------------------------------------------------------------------------- /external/HisToGene/Workflow.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/Workflow.PNG -------------------------------------------------------------------------------- /external/HisToGene/data/download.sh: -------------------------------------------------------------------------------- 1 | git clone https://github.com/almaan/her2st.git 2 | -------------------------------------------------------------------------------- /external/HisToGene/data/her_hvg_cut_1000.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/data/her_hvg_cut_1000.npy -------------------------------------------------------------------------------- /external/HisToGene/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/dataset.py -------------------------------------------------------------------------------- /external/HisToGene/model/download_checkpoint.txt: -------------------------------------------------------------------------------- 1 | https://drive.google.com/file/d/15Js-oGI5fScZwN0Xd_5FytL4UJP3i1eN/view?usp=sharing 2 | -------------------------------------------------------------------------------- /external/HisToGene/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/predict.py -------------------------------------------------------------------------------- /external/HisToGene/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/transformer.py -------------------------------------------------------------------------------- /external/HisToGene/tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/tutorial.ipynb -------------------------------------------------------------------------------- /external/HisToGene/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/utils.py -------------------------------------------------------------------------------- /external/HisToGene/vis_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/HisToGene/vis_model.py -------------------------------------------------------------------------------- /external/THItoGene/GATLayer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/GATLayer.py -------------------------------------------------------------------------------- /external/THItoGene/ODConv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/ODConv.py -------------------------------------------------------------------------------- /external/THItoGene/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/README.md -------------------------------------------------------------------------------- /external/THItoGene/THItoGene.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/THItoGene.yml -------------------------------------------------------------------------------- /external/THItoGene/data/download.sh: -------------------------------------------------------------------------------- 1 | git clone https://github.com/almaan/her2st.git -------------------------------------------------------------------------------- /external/THItoGene/data/her_hvg_cut_1000.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/data/her_hvg_cut_1000.npy -------------------------------------------------------------------------------- /external/THItoGene/data/skin_hvg_cut_1000.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/data/skin_hvg_cut_1000.npy -------------------------------------------------------------------------------- /external/THItoGene/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/dataset.py -------------------------------------------------------------------------------- /external/THItoGene/efficient_capsnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/efficient_capsnet.py -------------------------------------------------------------------------------- /external/THItoGene/graph_construction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/graph_construction.py -------------------------------------------------------------------------------- /external/THItoGene/model/download.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/model/download.txt -------------------------------------------------------------------------------- /external/THItoGene/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/predict.py -------------------------------------------------------------------------------- /external/THItoGene/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/requirements.txt -------------------------------------------------------------------------------- /external/THItoGene/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/train.py -------------------------------------------------------------------------------- /external/THItoGene/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/transformer.py -------------------------------------------------------------------------------- /external/THItoGene/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/utils.py -------------------------------------------------------------------------------- /external/THItoGene/vis_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/vis_model.py -------------------------------------------------------------------------------- /external/THItoGene/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/THItoGene/workflow.png -------------------------------------------------------------------------------- /external/cell_SSL/CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /external/cell_SSL/CONFIG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/CONFIG.md -------------------------------------------------------------------------------- /external/cell_SSL/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/CONTRIBUTING.md -------------------------------------------------------------------------------- /external/cell_SSL/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/LICENSE -------------------------------------------------------------------------------- /external/cell_SSL/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/README.md -------------------------------------------------------------------------------- /external/cell_SSL/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /external/cell_SSL/augmentations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/augmentations.py -------------------------------------------------------------------------------- /external/cell_SSL/convert_to_deit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/convert_to_deit.py -------------------------------------------------------------------------------- /external/cell_SSL/data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/data_utils.py -------------------------------------------------------------------------------- /external/cell_SSL/dataset_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/dataset_utils.py -------------------------------------------------------------------------------- /external/cell_SSL/main_lincls.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/main_lincls.py -------------------------------------------------------------------------------- /external/cell_SSL/main_moco.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/main_moco.py -------------------------------------------------------------------------------- /external/cell_SSL/moco/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved 2 | -------------------------------------------------------------------------------- /external/cell_SSL/moco/builder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/moco/builder.py -------------------------------------------------------------------------------- /external/cell_SSL/moco/loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/moco/loader.py -------------------------------------------------------------------------------- /external/cell_SSL/moco/optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/moco/optimizer.py -------------------------------------------------------------------------------- /external/cell_SSL/poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/poetry.lock -------------------------------------------------------------------------------- /external/cell_SSL/pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/pyproject.toml -------------------------------------------------------------------------------- /external/cell_SSL/transfer/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/transfer/README.md -------------------------------------------------------------------------------- /external/cell_SSL/transfer/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /external/cell_SSL/transfer/datasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/transfer/datasets.py -------------------------------------------------------------------------------- /external/cell_SSL/transfer/oxford_flowers_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/transfer/oxford_flowers_dataset.py -------------------------------------------------------------------------------- /external/cell_SSL/transfer/oxford_pets_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/transfer/oxford_pets_dataset.py -------------------------------------------------------------------------------- /external/cell_SSL/vits.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/cell_SSL/vits.py -------------------------------------------------------------------------------- /external/istar/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/LICENSE -------------------------------------------------------------------------------- /external/istar/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/README.md -------------------------------------------------------------------------------- /external/istar/aggregate_imputed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/aggregate_imputed.py -------------------------------------------------------------------------------- /external/istar/cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/cluster.py -------------------------------------------------------------------------------- /external/istar/connected_components.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/connected_components.py -------------------------------------------------------------------------------- /external/istar/data/markers/cell-type-template.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/data/markers/cell-type-template.tsv -------------------------------------------------------------------------------- /external/istar/data/markers/signature-score-template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/data/markers/signature-score-template.txt -------------------------------------------------------------------------------- /external/istar/differential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/differential.py -------------------------------------------------------------------------------- /external/istar/download_checkpoints.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/download_checkpoints.sh -------------------------------------------------------------------------------- /external/istar/download_demo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/download_demo.sh -------------------------------------------------------------------------------- /external/istar/enrich.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/enrich.py -------------------------------------------------------------------------------- /external/istar/extract_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/extract_features.py -------------------------------------------------------------------------------- /external/istar/get_mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/get_mask.py -------------------------------------------------------------------------------- /external/istar/hipt_4k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/hipt_4k.py -------------------------------------------------------------------------------- /external/istar/hipt_heatmap_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/hipt_heatmap_utils.py -------------------------------------------------------------------------------- /external/istar/hipt_model_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/hipt_model_utils.py -------------------------------------------------------------------------------- /external/istar/image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/image.py -------------------------------------------------------------------------------- /external/istar/impute.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/impute.py -------------------------------------------------------------------------------- /external/istar/impute_by_basic.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/impute_by_basic.py -------------------------------------------------------------------------------- /external/istar/marker_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/marker_score.py -------------------------------------------------------------------------------- /external/istar/pixannot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/pixannot.py -------------------------------------------------------------------------------- /external/istar/plot_imputed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/plot_imputed.py -------------------------------------------------------------------------------- /external/istar/plot_spots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/plot_spots.py -------------------------------------------------------------------------------- /external/istar/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/preprocess.py -------------------------------------------------------------------------------- /external/istar/reduce_dim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/reduce_dim.py -------------------------------------------------------------------------------- /external/istar/reorganize_imputed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/reorganize_imputed.py -------------------------------------------------------------------------------- /external/istar/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/requirements.txt -------------------------------------------------------------------------------- /external/istar/rescale.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/rescale.py -------------------------------------------------------------------------------- /external/istar/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/run.sh -------------------------------------------------------------------------------- /external/istar/run_demo.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/run_demo.sh -------------------------------------------------------------------------------- /external/istar/select_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/select_genes.py -------------------------------------------------------------------------------- /external/istar/structural_similarity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/structural_similarity.py -------------------------------------------------------------------------------- /external/istar/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/train.py -------------------------------------------------------------------------------- /external/istar/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/utils.py -------------------------------------------------------------------------------- /external/istar/vision_transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/vision_transformer.py -------------------------------------------------------------------------------- /external/istar/vision_transformer4k.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/vision_transformer4k.py -------------------------------------------------------------------------------- /external/istar/visual.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/istar/visual.py -------------------------------------------------------------------------------- /external/mclSTExp/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/README.md -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/BLEEP_inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/BLEEP_inference.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/BLEEP_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/BLEEP_main.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/BLEEP_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/BLEEP_overview.png -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/LICENSE -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/config.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/dataset.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/models.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/modules.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/preprocess.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/preprocess.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/baselines/Bleep/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/Bleep/utils.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/HIST2ST.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/HIST2ST.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/HIST2ST_train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/HIST2ST_train.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/NB_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/NB_module.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/Workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/Workflow.png -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/dataset.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/gcn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/gcn.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/graph_construction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/graph_construction.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/predict.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/run_trained_models.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/run_trained_models.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/transformer.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/tutorial.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/baselines/His2ST/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/His2ST/utils.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/LICENSE -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/Workflow.PNG: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/Workflow.PNG -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/dataset.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/predict.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/transformer.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/tutorial.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/utils.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/HisToGene/vis_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/HisToGene/vis_model.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/ReadMe: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/GATLayer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/GATLayer.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/ODConv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/ODConv.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/THItoGene.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/THItoGene.yml -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/dataset.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/efficient_capsnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/efficient_capsnet.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/graph_construction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/graph_construction.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/predict.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/requirements.txt -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/train.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/transformer.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/utils: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/utils -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/vis_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/vis_model.py -------------------------------------------------------------------------------- /external/mclSTExp/baselines/THItoGene/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/baselines/THItoGene/workflow.png -------------------------------------------------------------------------------- /external/mclSTExp/data/1000hvg_common.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/data/1000hvg_common.pkl -------------------------------------------------------------------------------- /external/mclSTExp/data/download.sh: -------------------------------------------------------------------------------- 1 | git clone https://github.com/almaan/her2st.git 2 | -------------------------------------------------------------------------------- /external/mclSTExp/data/her_hvg_cut_1000.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/data/her_hvg_cut_1000.npy -------------------------------------------------------------------------------- /external/mclSTExp/data/skin_hvg_cut_1000.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/data/skin_hvg_cut_1000.npy -------------------------------------------------------------------------------- /external/mclSTExp/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/dataset.py -------------------------------------------------------------------------------- /external/mclSTExp/evel_cscc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/evel_cscc.py -------------------------------------------------------------------------------- /external/mclSTExp/evel_her2st.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/evel_her2st.py -------------------------------------------------------------------------------- /external/mclSTExp/evel_visium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/evel_visium.py -------------------------------------------------------------------------------- /external/mclSTExp/hvg_cscc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/hvg_cscc.py -------------------------------------------------------------------------------- /external/mclSTExp/hvg_her2st.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/hvg_her2st.py -------------------------------------------------------------------------------- /external/mclSTExp/hvg_visium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/hvg_visium.py -------------------------------------------------------------------------------- /external/mclSTExp/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/model.py -------------------------------------------------------------------------------- /external/mclSTExp/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/train.py -------------------------------------------------------------------------------- /external/mclSTExp/tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/tutorial.ipynb -------------------------------------------------------------------------------- /external/mclSTExp/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/utils.py -------------------------------------------------------------------------------- /external/mclSTExp/workflow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/external/mclSTExp/workflow.png -------------------------------------------------------------------------------- /full_pipeline_script.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/full_pipeline_script.py -------------------------------------------------------------------------------- /method.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/method.jpg -------------------------------------------------------------------------------- /scellst/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/__init__.py -------------------------------------------------------------------------------- /scellst/bench/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/bench/bench_data_handler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/bench_data_handler.py -------------------------------------------------------------------------------- /scellst/bench/bench_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/bench_dataset.py -------------------------------------------------------------------------------- /scellst/bench/data_formatting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/data_formatting.py -------------------------------------------------------------------------------- /scellst/bench/utils_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/utils_data.py -------------------------------------------------------------------------------- /scellst/bench/utils_histogene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/utils_histogene.py -------------------------------------------------------------------------------- /scellst/bench/utils_istar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/utils_istar.py -------------------------------------------------------------------------------- /scellst/bench/utils_mclstexp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/utils_mclstexp.py -------------------------------------------------------------------------------- /scellst/bench/utils_thitogene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/bench/utils_thitogene.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/cellhest_adapter/aggregation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/aggregation.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/cell_hest_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/cell_hest_data.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/cell_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/cell_utils.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/data_mixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/data_mixin.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/h5_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/h5_utils.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/plot_mixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/plot_mixin.py -------------------------------------------------------------------------------- /scellst/cellhest_adapter/processing_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/cellhest_adapter/processing_utils.py -------------------------------------------------------------------------------- /scellst/constant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/constant.py -------------------------------------------------------------------------------- /scellst/dataset/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/dataset/batch_sampler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/batch_sampler.py -------------------------------------------------------------------------------- /scellst/dataset/cell_image_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/cell_image_dataset.py -------------------------------------------------------------------------------- /scellst/dataset/data_handler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/data_handler.py -------------------------------------------------------------------------------- /scellst/dataset/data_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/data_module.py -------------------------------------------------------------------------------- /scellst/dataset/dataset_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/dataset_utils.py -------------------------------------------------------------------------------- /scellst/dataset/gene_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/gene_utils.py -------------------------------------------------------------------------------- /scellst/dataset/torch_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/dataset/torch_dataset.py -------------------------------------------------------------------------------- /scellst/lightning_model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/lightning_model/base_lightning_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/lightning_model/base_lightning_model.py -------------------------------------------------------------------------------- /scellst/lightning_model/gene_lightning_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/lightning_model/gene_lightning_model.py -------------------------------------------------------------------------------- /scellst/metrics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/metrics/gene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/metrics/gene.py -------------------------------------------------------------------------------- /scellst/metrics/metric_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/metrics/metric_utils.py -------------------------------------------------------------------------------- /scellst/model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/model/base_mil_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/model/base_mil_model.py -------------------------------------------------------------------------------- /scellst/model/instance_mil_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/model/instance_mil_distribution.py -------------------------------------------------------------------------------- /scellst/model/instance_mil_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/model/instance_mil_model.py -------------------------------------------------------------------------------- /scellst/module/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/module/distributions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/module/distributions.py -------------------------------------------------------------------------------- /scellst/module/gene_predictor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/module/gene_predictor.py -------------------------------------------------------------------------------- /scellst/module/image_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/module/image_encoder.py -------------------------------------------------------------------------------- /scellst/plots/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/plots/plot_hest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/plots/plot_hest.py -------------------------------------------------------------------------------- /scellst/plots/plot_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/plots/plot_metrics.py -------------------------------------------------------------------------------- /scellst/plots/plot_spatial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/plots/plot_spatial.py -------------------------------------------------------------------------------- /scellst/plots/plot_ssl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/plots/plot_ssl.py -------------------------------------------------------------------------------- /scellst/predict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/predict.py -------------------------------------------------------------------------------- /scellst/submit_function.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/submit_function.py -------------------------------------------------------------------------------- /scellst/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/train.py -------------------------------------------------------------------------------- /scellst/trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/trainer.py -------------------------------------------------------------------------------- /scellst/type.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/type.py -------------------------------------------------------------------------------- /scellst/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /scellst/utils/img_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/utils/img_utils.py -------------------------------------------------------------------------------- /scellst/utils/io_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/utils/io_utils.py -------------------------------------------------------------------------------- /scellst/utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/scellst/utils/utils.py -------------------------------------------------------------------------------- /simulation/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /simulation/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/data_loader.py -------------------------------------------------------------------------------- /simulation/data_preparation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/data_preparation.py -------------------------------------------------------------------------------- /simulation/decoupler_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/decoupler_utils.py -------------------------------------------------------------------------------- /simulation/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/main.py -------------------------------------------------------------------------------- /simulation/sim_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/sim_data_utils.py -------------------------------------------------------------------------------- /simulation/supervised_lightning_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/supervised_lightning_model.py -------------------------------------------------------------------------------- /simulation/supervised_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/simulation/supervised_model.py -------------------------------------------------------------------------------- /training_tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/loicchadoutaud/sCellST/HEAD/training_tutorial.ipynb --------------------------------------------------------------------------------