.DS_Store
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
Garfield_Model_Parameters.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
Garfield/.gitignore
Garfield/__init__.py
Garfield/_settings.py
Garfield/_version.py
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/analysis/__init__.py
Garfield/analysis/calc_neighbor_prop.py
Garfield/analysis/calc_niches_enrich.py
Garfield/analysis/calc_niches_marker.py
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/data/gene_anno/protein_gene_conversion.csv
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/plot/__init__.py
Garfield/plot/spatial_plot.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
docs/.gitignore
docs/Makefile
docs/environment.yml
docs/make.bat
docs/requirements.txt
docs/source/API.rst
docs/source/About Garfield.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/Garfield_framework.png
docs/source/_static/img/garfield_icon.svg
docs/source/_static/img/logo_garfield.png
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.EarlyStopping.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
docs/source/generated/Garfield.trainer.print_progress.rst
docs/source/tutorial/01.panc8_all_batch_correction.ipynb
docs/source/tutorial/02.panc_mapping.ipynb
docs/source/tutorial/03.10x_pbmc_paired_scMulti_analysis.ipynb
docs/source/tutorial/04.Garfield_spatia_molecular_niche_seqFISH_Mouse_Organogenesis.ipynb
docs/source/tutorial/05.Garfield_spatial_niche_slideseqv2_mouse_hippocampus.ipynb
docs/source/tutorial/06.Garfield_spMulti_mouse_brain.ipynb
imgs/Garfield_framework2.png