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Garfield_Model_Parameters.md
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MANIFEST.in
README.md
requirements.txt
setup.py
Garfield/.gitignore
Garfield/__init__.py
Garfield/_settings.py
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Garfield.egg-info/PKG-INFO
Garfield.egg-info/SOURCES.txt
Garfield.egg-info/dependency_links.txt
Garfield.egg-info/requires.txt
Garfield.egg-info/top_level.txt
Garfield/.idea/misc.xml
Garfield/.idea/modules.xml
Garfield/.idea/workspace.xml
Garfield/.idea/inspectionProfiles/profiles_settings.xml
Garfield/data/__init__.py
Garfield/data/dataloaders.py
Garfield/data/dataprocessors.py
Garfield/data/datareaders.py
Garfield/data/datasets.py
Garfield/data/gene_anno/hg19_genes.bed
Garfield/data/gene_anno/hg38_genes.bed
Garfield/data/gene_anno/mm10_genes.bed
Garfield/data/gene_anno/mm9_genes.bed
Garfield/model/Garfield.py
Garfield/model/__init__.py
Garfield/model/basemodelmixin.py
Garfield/model/utils.py
Garfield/modules/GNNModelVAE.py
Garfield/modules/__init__.py
Garfield/modules/loss.py
Garfield/modules/utils.py
Garfield/nn/__init__.py
Garfield/nn/decoders.py
Garfield/nn/encoders.py
Garfield/nn/utils.py
Garfield/preprocessing/__init__.py
Garfield/preprocessing/_graph.py
Garfield/preprocessing/_utils.py
Garfield/preprocessing/adj_construction.py
Garfield/preprocessing/match_utils.py
Garfield/preprocessing/preprocess.py
Garfield/preprocessing/preprocess_utils.py
Garfield/trainer/__init__.py
Garfield/trainer/basetrainermixin.py
Garfield/trainer/metrics.py
Garfield/trainer/trainer.py
Garfield/trainer/utils.py
data/pbmc3k_processed.h5ad
docs/Makefile
docs/environment.yml
docs/make.bat
docs/requirements.txt
docs/source/01.panc8_all_batch_correction.ipynb
docs/source/02.panc_mapping.ipynb
docs/source/03.10x_pbmc_paired_scMulti_analysis.ipynb
docs/source/04.Garfield_spatia_molecular_niche_seqFISH_Mouse_Organogenesis.ipynb
docs/source/05.Garfield_spatial_niche_slideseqv2_mouse_hippocampus.ipynb
docs/source/06.Garfield_spMulti_mouse_brain.ipynb
docs/source/API.rst
docs/source/About Garfield.rst
docs/source/Basic concepts.rst
docs/source/Citation.rst
docs/source/Installation.rst
docs/source/Makefile
docs/source/Release notes.rst
docs/source/conf.py
docs/source/index.rst
docs/source/make.bat
docs/source/_autosummary/Garfield.settings.set_figure_params.rst
docs/source/_autosummary/Garfield.settings.set_gf_params.rst
docs/source/_autosummary/Garfield.settings.set_workdir.rst
docs/source/_ext/edit_on_github.py
docs/source/_static/img/Cartoon_Cat_Starry_Night.pdf
docs/source/_static/img/Cartoon_Cat_Starry_Night.png
docs/source/_static/img/DALL·E 2024-07-06 17.40.03 - Create a cartoon-style image of an orange tabby cat with a chubby body, sitting on a rock and gazing up at a starry night sky. The cat should have exp.webp
docs/source/_static/img/Garfield_framework.png
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docs/source/generated/Garfield.data.GraphAnnTorchDataset.rst
docs/source/generated/Garfield.data.edge_level_split.rst
docs/source/generated/Garfield.data.initialize_dataloaders.rst
docs/source/generated/Garfield.data.node_level_split_mask.rst
docs/source/generated/Garfield.data.prepare_data.rst
docs/source/generated/Garfield.model.Garfield.Garfield.rst
docs/source/generated/Garfield.model.utils.weighted_knn_trainer.rst
docs/source/generated/Garfield.model.utils.weighted_knn_transfer.rst
docs/source/generated/Garfield.modules.GNNModelVAE.rst
docs/source/generated/Garfield.modules.compute_contrastive_clusterloss.rst
docs/source/generated/Garfield.modules.compute_contrastive_instanceloss.rst
docs/source/generated/Garfield.modules.compute_edge_recon_loss.rst
docs/source/generated/Garfield.modules.compute_kl_reg_loss.rst
docs/source/generated/Garfield.modules.compute_omics_recon_mmd_loss.rst
docs/source/generated/Garfield.modules.compute_omics_recon_mse_loss.rst
docs/source/generated/Garfield.nn.DSBatchNorm.rst
docs/source/generated/Garfield.nn.GATDecoder.rst
docs/source/generated/Garfield.nn.GATEncoder.rst
docs/source/generated/Garfield.nn.GCNDecoder.rst
docs/source/generated/Garfield.nn.GCNEncoder.rst
docs/source/generated/Garfield.preprocessing.DataProcess.rst
docs/source/generated/Garfield.preprocessing.gene_scores.rst
docs/source/generated/Garfield.preprocessing.get_nearest_neighbors.rst
docs/source/generated/Garfield.preprocessing.preprocessing.rst
docs/source/generated/Garfield.preprocessing.preprocessing_adt.rst
docs/source/generated/Garfield.preprocessing.preprocessing_atac.rst
docs/source/generated/Garfield.preprocessing.preprocessing_rna.rst
docs/source/generated/Garfield.trainer.GarfieldTrainer.rst
docs/source/generated/Garfield.trainer.eval_metrics.rst
docs/source/generated/Garfield.trainer.plot_eval_metrics.rst
imgs/Garfield_framework2.png
test/02.run_ccVAE_panc8_all.ipynb
test/ATAC_10x_pbmc_analysis-Copy2.ipynb
test/ATAC_10x_pbmc_analysis-paired.ipynb
test/ATAC_10x_pbmc_analysis.ipynb
test/ILC_T_mapping_Garfield.ipynb
test/human_embryo_integration.ipynb
test/panc_mapping.ipynb