Modeling Embryo–Endometrial Interface Recapitulating Human Embryo Implantation

Scripts and notebooks related to the snRNA-seq analysis part of the paper.

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Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
1_ari_org_sample_integration.ipynb		1_ari_org_sample_integration.ipynb
2.0_ga_convert_to_h5seurat.ipynb		2.0_ga_convert_to_h5seurat.ipynb
2.1_wg_integrate_metadata_convert_to_h5ad_h5seurat.ipynb		2.1_wg_integrate_metadata_convert_to_h5ad_h5seurat.ipynb
2.2_QC_and_downsizing_cell_atlas.ipynb		2.2_QC_and_downsizing_cell_atlas.ipynb
3_integration_arima_and_downsampled_atlases.ipynb		3_integration_arima_and_downsampled_atlases.ipynb
4_ari_org_annotation.ipynb		4_ari_org_annotation.ipynb
4_ari_org_annotation_revision1.ipynb		4_ari_org_annotation_revision1.ipynb
5_integration_arima_and_GA_organoid.ipynb		5_integration_arima_and_GA_organoid.ipynb
6.0_convert_seurat_scanpy.ipynb		6.0_convert_seurat_scanpy.ipynb
6.1_generate_RNA_velocity_values.sh		6.1_generate_RNA_velocity_values.sh
6.2_combine_loom_files.ipynb		6.2_combine_loom_files.ipynb
6.3_RNA_velocity_analysis.ipynb		6.3_RNA_velocity_analysis.ipynb
7_integration_arima_and_downsampled_atlases-Revision1.ipynb		7_integration_arima_and_downsampled_atlases-Revision1.ipynb
8_cellchat_signaling_and_contact_epi_endo_stro.ipynb		8_cellchat_signaling_and_contact_epi_endo_stro.ipynb
LICENSE		LICENSE
README.md		README.md
functions_nagai.R		functions_nagai.R
run_cellranger.sh		run_cellranger.sh