LICENSE.txt
MANIFEST.in
README.md
README.rst
pyproject.toml
setup.py
spared/spared/__init__.py
spared/spared/gtftools.py
spared/spared.egg-info/PKG-INFO
spared/spared.egg-info/SOURCES.txt
spared/spared.egg-info/dependency_links.txt
spared/spared.egg-info/top_level.txt
spared/spared/PublicDatabase/README_template.md
spared/spared/configs/10xgenomic_human_brain.json
spared/spared/configs/10xgenomic_human_breast_cancer.json
spared/spared/configs/10xgenomic_mouse_brain_coronal.json
spared/spared/configs/10xgenomic_mouse_brain_sagittal_anterior.json
spared/spared/configs/10xgenomic_mouse_brain_sagittal_posterior.json
spared/spared/configs/abalo_human_squamous_cell_carcinoma.json
spared/spared/configs/add_hex_geometry.py
spared/spared/configs/add_organism.py
spared/spared/configs/batiuk_human_brain.json
spared/spared/configs/erickson_human_prostate_cancer_p1.json
spared/spared/configs/erickson_human_prostate_cancer_p2.json
spared/spared/configs/fan_mouse_brain_coronal.json
spared/spared/configs/fan_mouse_olfatory_bulb.json
spared/spared/configs/hudson_human_brain.json
spared/spared/configs/mirzazadeh_human_colon_p1.json
spared/spared/configs/mirzazadeh_human_colon_p2.json
spared/spared/configs/mirzazadeh_human_pediatric_brain_tumor_p1.json
spared/spared/configs/mirzazadeh_human_pediatric_brain_tumor_p2.json
spared/spared/configs/mirzazadeh_human_prostate_cancer.json
spared/spared/configs/mirzazadeh_human_small_intestine.json
spared/spared/configs/mirzazadeh_mouse_bone.json
spared/spared/configs/mirzazadeh_mouse_brain.json
spared/spared/configs/mirzazadeh_mouse_brain_p1.json
spared/spared/configs/mirzazadeh_mouse_brain_p2.json
spared/spared/configs/parigi_mouse_intestine.json
spared/spared/configs/vicari_human_striatium.json
spared/spared/configs/vicari_mouse_brain.json
spared/spared/configs/villacampa_kidney_organoid.json
spared/spared/configs/villacampa_lung_organoid.json
spared/spared/configs/villacampa_mouse_brain.json
spared/spared/data/annotations/gencode.v43.basic.annotation.gtf.gz
spared/spared/data/annotations/gencode.vM33.basic.annotation.gtf.gz
spared/spared/data/annotations/gene_length.txt
spared/spared/data/annotations/gene_length_mouse.txt
spared/spared/data/annotations/mapping_HUGO_2_Ensemble.txt
spared/spared/data/annotations/mart_export.txt
spared/spared/data/annotations/old_gencode.v43.basic.annotation.gtf.gz
spared/spared/data/annotations/old_gencode.vM33.basic.annotation.gtf.gz
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_A1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_A1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_B1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_B1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_C1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_C1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_D1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-038_D1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_A1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_A1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_B1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_B1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_C1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_C1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_D1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11L12-109_D1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_A1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_A1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_B1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_B1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_C1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_C1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_D1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T16-085_D1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T17-101_A1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T17-101_A1/spatial/scalefactors_json.json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T17-101_B1/spatial/scalefactors_json (1).json
spared/spared/data/vicari_data/vicari_mouse_brain/V11T17-101_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_A1/V19T26-103-A1.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_B1/V19T26-103-B1.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_C1/V19T26-103-C1.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_D1/V19T26-103-D1.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/HGSC/V19T26-103_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_A1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_B1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_C1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_D1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/archivalcancer/V10F24-111_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/kidneyorganoid/organoid_selection.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/kidneyorganoid/V19D02-085_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/kidneyorganoid/V19D02-085_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/kidneyorganoid/V19D02-085_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lung_SARS-CoV-2/V10F24-110_C1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lung_SARS-CoV-2/V10F24-110_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lung_SARS-CoV-2/V10F24-110_D1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lung_SARS-CoV-2/V10F24-110_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungcellmarkers/README.md
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungorganoid/organoid_selection.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungorganoid/V19D02-088_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungorganoid/V19D02-088_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungorganoid/V19D02-088_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/lungorganoid/V19D02-088_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF1_public_data/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF2_public_data_S1_Sagittal_anterior/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF3_public_data_S1_Sagittal_posterior/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF4_public_data_S2_Sagittal_anterior/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF5_public_data_S2_Sagittal_posterior/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF6/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/FF7/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-078_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-078_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-078_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-078_D1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-110_A1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-110_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-110_B1/cutadapt_log.txt
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V10F24-110_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_kidney_organoid/data/mousebrain/V19T26-039_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_lung_organoid/data/lungorganoid/organoid_selection.txt
spared/spared/data/villacampa_data/villacampa_lung_organoid/data/lungorganoid/V19D02-088_A1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_lung_organoid/data/lungorganoid/V19D02-088_B1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_lung_organoid/data/lungorganoid/V19D02-088_C1/spatial/scalefactors_json.json
spared/spared/data/villacampa_data/villacampa_lung_organoid/data/lungorganoid/V19D02-088_D1/spatial/scalefactors_json.json
spared/spared/dataloaders/__init__.py
spared/spared/dataloaders/dataloaders.py
spared/spared/datasets/__init__.py
spared/spared/datasets/datasets.py
spared/spared/denoising/__init__.py
spared/spared/denoising/denoising.py
spared/spared/filtering/__init__.py
spared/spared/filtering/filtering.py
spared/spared/gene_features/__init__.py
spared/spared/gene_features/gene_features.py
spared/spared/graph_operations/__init__.py
spared/spared/graph_operations/graph_operations.py
spared/spared/layer_operations/__init__.py
spared/spared/layer_operations/layer_operations.py
spared/spared/metrics/__init__.py
spared/spared/metrics/metrics.py
spared/spared/models/__init__.py
spared/spared/models/models.py
spared/spared/plotting/__init__.py
spared/spared/plotting/plotting.py
spared/spared/readers/AbaloReader.py
spared/spared/readers/AnderssonReader.py
spared/spared/readers/AspReader.py
spared/spared/readers/BatiukReader.py
spared/spared/readers/EricksonReader.py
spared/spared/readers/FanReader.py
spared/spared/readers/KvastadReader.py
spared/spared/readers/MirzazadehReader.py
spared/spared/readers/MoncadaReader.py
spared/spared/readers/ParigiReader.py
spared/spared/readers/STNetReader.py
spared/spared/readers/VicariReader.py
spared/spared/readers/VillacampaReader.py
spared/spared/readers/VisiumReader.py
spared/spared/readers/__init__.py
spared/spared/spackle/dataset.py
spared/spared/spackle/main.py
spared/spared/spackle/model.py
spared/spared/spackle/utils.py
spared/spared/spot_features/__init__.py
spared/spared/spot_features/spot_features.py
spared/spared/tests/__init__.py
spared/spared/tests/test_dataloaders.py
spared/spared/tests/test_dataset.py
spared/spared/tests/test_denoising.py
spared/spared/tests/test_filtering.py
spared/spared/tests/test_gene_features.py
spared/spared/tests/test_graph_operations.py
spared/spared/tests/test_layer_operations.py
spared/spared/tests/test_log_pred_img.py
spared/spared/tests/test_metrics.py
spared/spared/tests/test_models.py
spared/spared/tests/test_plotting.py
spared/spared/tests/test_spot_features.py
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-14-10-41-01/script_params.json
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-14-11-04-44/script_params.json
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-14-11-04-44/testing_results.txt
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-14-11-31-31/script_params.json
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-14-11-31-31/testing_results.txt
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-21-13-34-37/script_params.json
spared/spared/tests/imput_results/vicari_mouse_brain/2024-08-21-13-34-37/testing_results.txt
spared/spared/tests/imput_results/villacampa_lung_organoid/2024-07-31-17-58-59/script_params.json
spared/spared/tests/imput_results/villacampa_lung_organoid/2024-07-31-17-58-59/testing_results.txt
spared/spared/tests/imput_results/villacampa_lung_organoid/2024-07-31-18-00-06/script_params.json
spared/spared/tests/imput_results/villacampa_lung_organoid/2024-07-31-18-00-06/testing_results.txt
spared/spared/tests/imput_results/villacampa_lung_organoid/2024-07-31-19-27-49/script_params.json
spared/spared/tests/processed_data/vicari_data/vicari_mouse_brain/2024-08-11-18-40-39/parameters.json
spared/tutorials/imput_results/vicari_mouse_brain/2024-08-11-19-44-40/script_params.json
spared/tutorials/imput_results/vicari_mouse_brain/2024-08-11-20-18-49/script_params.json
spared/tutorials/imput_results/vicari_mouse_brain/2024-08-11-20-18-49/testing_results.txt
spared/tutorials/processed_data/vicari_data/vicari_mouse_brain/2024-08-11-18-40-39/parameters.json