Cell-Cell-Communication using NEST: NEural network on Spatial Transcriptomics.

Contact: Author: fatema.zohora@uhn.ca Supervisor: Gregory.Schwartz@uhn.ca (https://schwartzlab.ca/)

Name		Name	Last commit message	Last commit date
Latest commit History 2,006 Commits
demo		demo
label		label
AnnoSpat_preprocess.py		AnnoSpat_preprocess.py
CCC_RGCN_model_run.py		CCC_RGCN_model_run.py
CCC_gat.py		CCC_gat.py
CCC_gat_split.py		CCC_gat_split.py
CCC_gat_split_v2.py		CCC_gat_split_v2.py
CCC_train_ST.py		CCC_train_ST.py
COMMOT_synthetic.py		COMMOT_synthetic.py
CellNEST_synthetic_equidistant_alternate_cutoff_ccc_list_all.py		CellNEST_synthetic_equidistant_alternate_cutoff_ccc_list_all.py
CellNEST_synthetic_mechanistic_list_all.py		CellNEST_synthetic_mechanistic_list_all.py
CellNEST_synthetic_merfish_ccc_list_all.py		CellNEST_synthetic_merfish_ccc_list_all.py
CellNEST_synthetic_mixture_alternate_cutoff_ccc_list_all.py		CellNEST_synthetic_mixture_alternate_cutoff_ccc_list_all.py
CellNEST_synthetic_mixture_ccc_list_all.py		CellNEST_synthetic_mixture_ccc_list_all.py
CellNEST_synthetic_randomCCC_list_all.py		CellNEST_synthetic_randomCCC_list_all.py
CellNEST_synthetic_uniform_alternate_cutoff_ccc_list_all.py		CellNEST_synthetic_uniform_alternate_cutoff_ccc_list_all.py
CellNEST_synthetic_visium_ccc_list_all.py		CellNEST_synthetic_visium_ccc_list_all.py
ESMfold_data_preprocess.py		ESMfold_data_preprocess.py
LRBind_postprocess_ROI.py		LRBind_postprocess_ROI.py
LRBind_pre_vs_post_filtered.py		LRBind_pre_vs_post_filtered.py
LRbind_VGAE_model.py		LRbind_VGAE_model.py
LRbind_alphafold.py		LRbind_alphafold.py
LRbind_build_intraNW.py		LRbind_build_intraNW.py
LRbind_data_preprocess.py		LRbind_data_preprocess.py
LRbind_data_preprocess_geneCorrKNN.py		LRbind_data_preprocess_geneCorrKNN.py
LRbind_data_preprocess_geneCorrKNN_anndata.py		LRbind_data_preprocess_geneCorrKNN_anndata.py
LRbind_data_preprocess_intraNW.py		LRbind_data_preprocess_intraNW.py
LRbind_ligand_upstream_genes.py		LRbind_ligand_upstream_genes.py
LRbind_model.py		LRbind_model.py
LRbind_model_heterogenous.py		LRbind_model_heterogenous.py
LRbind_model_split.py		LRbind_model_split.py
LRbind_model_tanh.py		LRbind_model_tanh.py
LRbind_plot_AlphaFold_scores.py		LRbind_plot_AlphaFold_scores.py
LRbind_postprocess.py		LRbind_postprocess.py
LRbind_postprocess_PCA.py		LRbind_postprocess_PCA.py
LRbind_postprocess_ROI_downstream.py		LRbind_postprocess_ROI_downstream.py
LRbind_postprocess_downstream.py		LRbind_postprocess_downstream.py
LRbind_postprocess_downstream_DEG.py		LRbind_postprocess_downstream_DEG.py
LRbind_postprocess_post_embFusion.py		LRbind_postprocess_post_embFusion.py
LRbind_postprocess_remFromDB.py		LRbind_postprocess_remFromDB.py
LRbind_postprocess_split_graphs.py		LRbind_postprocess_split_graphs.py
LRbind_postprocess_testdata.py		LRbind_postprocess_testdata.py
LRbind_postprocess_up_down_DEG_clustered.py		LRbind_postprocess_up_down_DEG_clustered.py
LRbind_postprocess_upstream_downstream_DEG.py		LRbind_postprocess_upstream_downstream_DEG.py
LRbind_postprocess_with_embFusion.py		LRbind_postprocess_with_embFusion.py
LRbind_postprocess_with_embFusion_multiple_samples.py		LRbind_postprocess_with_embFusion_multiple_samples.py
LRbind_preprocess_upstream_downstream_DEG.py		LRbind_preprocess_upstream_downstream_DEG.py
LRbind_receptor_downstream_gene.py		LRbind_receptor_downstream_gene.py
LRbind_run.py		LRbind_run.py
MESSI_PDAC.py		MESSI_PDAC.py
NEST_CRC_chiSquare_hypergeometric_test.py		NEST_CRC_chiSquare_hypergeometric_test.py
NEST_Visium_HD_segmentation.py		NEST_Visium_HD_segmentation.py
NEST_data_preprocess.py		NEST_data_preprocess.py
NEST_data_preprocess_big.py		NEST_data_preprocess_big.py
NEST_interactive.py		NEST_interactive.py
NEST_output_by_component.py		NEST_output_by_component.py
NEST_output_postprocess_rankProduct.py		NEST_output_postprocess_rankProduct.py
NEST_output_visualization.py		NEST_output_visualization.py
NEST_output_visualization_rank_product.py		NEST_output_visualization_rank_product.py
NEST_visualize_HumanLymphNode.py		NEST_visualize_HumanLymphNode.py
Niches_synthetic.R		Niches_synthetic.R
PDAC_140694_niches.R		PDAC_140694_niches.R
PDAC_64630_niches.R		PDAC_64630_niches.R
PDAC_COMMOT.py		PDAC_COMMOT.py
PDAC_COMMOT_relay.py		PDAC_COMMOT_relay.py
PDAC_Niches_relay.py		PDAC_Niches_relay.py
QC_xenium.py		QC_xenium.py
README.md		README.md
VGAEModel_LRbind.py		VGAEModel_LRbind.py
apply_GSEA.py		apply_GSEA.py
boxplot_cluster_intersect_signature_bySpots.py		boxplot_cluster_intersect_signature_bySpots.py
cellranger_output.py		cellranger_output.py
cellranger_output_2.py		cellranger_output_2.py
cellranger_output_3.py		cellranger_output_3.py
cellranger_output_4.py		cellranger_output_4.py
cluster_evaluation_calculate_v2.py		cluster_evaluation_calculate_v2.py
cluster_intersect_signature.py		cluster_intersect_signature.py
commot_synthetic_equidistant_ccc_list_all.py		commot_synthetic_equidistant_ccc_list_all.py
commot_synthetic_mechanistic_ccc_list_all.py		commot_synthetic_mechanistic_ccc_list_all.py
commot_synthetic_randomCCC_ccc_list_all.py		commot_synthetic_randomCCC_ccc_list_all.py
confidence_interval_NEST.py		confidence_interval_NEST.py
cytosignal_human_lymph.R		cytosignal_human_lymph.R
cytosignal_postprocess_mechanistic.py		cytosignal_postprocess_mechanistic.py
cytosignal_postprocessing.py		cytosignal_postprocessing.py
cytosignal_preprocess_human_lymph.py		cytosignal_preprocess_human_lymph.py
cytosignal_preprocess_synthetic.py		cytosignal_preprocess_synthetic.py
cytosignal_preprocess_synthetic_mechanistic.py		cytosignal_preprocess_synthetic_mechanistic.py
cytosignal_run.R		cytosignal_run.R
cytosignal_synthetic.R		cytosignal_synthetic.R
data_preprocess.py		data_preprocess.py
data_preprocess_NEST_visium_hd.py		data_preprocess_NEST_visium_hd.py
data_preprocess_intra_NEST.py		data_preprocess_intra_NEST.py
database_preprocess.py		database_preprocess.py
embFusion.py		embFusion.py
embFusion_train_util.py		embFusion_train_util.py
embFusion_validation.py		embFusion_validation.py
equallySpaced.py		equallySpaced.py
equallySpacedStroma.py		equallySpacedStroma.py
equallySpaced_Cells_in_Spot.py		equallySpaced_Cells_in_Spot.py
equallySpaced_Cells_in_Spot_multiple_lr.py		equallySpaced_Cells_in_Spot_multiple_lr.py

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