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downsample
downsample
 
 
new_tangram_mapping
new_tangram_mapping
 
 
Clustering_on_mapping_data.ipynb
Clustering_on_mapping_data.ipynb
 
 
SCTransform_Example.ipynb
SCTransform_Example.ipynb
 
 
STABMAP.ipynb
STABMAP.ipynb
 
 
TopicModeling_liver.ipynb
TopicModeling_liver.ipynb
 
 
Visualization_Ileum_deg_dist.ipynb
Visualization_Ileum_deg_dist.ipynb
 
 
Visualization_Vizgen_liver2.ipynb
Visualization_Vizgen_liver2.ipynb
 
 
Visualization_Vizgen_liver_crop_coordinates.ipynb
Visualization_Vizgen_liver_crop_coordinates.ipynb
 
 
correlation_tangram_spatial_liver.ipynb
correlation_tangram_spatial_liver.ipynb
 
 
day7_DE_analysis.ipynb
day7_DE_analysis.ipynb
 
 
filtersteps_clustering.py
filtersteps_clustering.py
 
 
find_cell_type.py
find_cell_type.py
 
 
learn_xgboost .ipynb
learn_xgboost .ipynb
 
 
mnnCorrect_immunity_ileum_mapping.ipynb
mnnCorrect_immunity_ileum_mapping.ipynb
 
 
plot_umap.py
plot_umap.py
 
 
readme
readme
 
 
remove_blank_genes.py
remove_blank_genes.py
 
 
sctransform_clustering_analysis_on_sc_sp_liver.ipynb
sctransform_clustering_analysis_on_sc_sp_liver.ipynb
 
 
seqFISH_scRNA_correlation.ipynb
seqFISH_scRNA_correlation.ipynb
 
 
tangram_mapping_Mouse_liver.ipynb
tangram_mapping_Mouse_liver.ipynb
 
 
transfer_of_sc_PCs_to_sp.ipynb
transfer_of_sc_PCs_to_sp.ipynb
 
 

readme

a=sc.read_h5ad('sc_liver_data.h5ad')
b=a.X.toarray()
df=pd.DataFrame(data=b.transpose(), index=a.var_names , columns=a.obs_names)
df.to_csv("sc_liver_data_ori.csv")

spatial data 

1) spatial_module/processed_vizgen_liver/mapping/Blank_genes_removed.csv
2) spatial_module/input_vizgen_liver_fourth_quadrant/spatial_quadrant.h5ad


single cell data 
1) spatial_module/processed_vizgen_liver/mapping/countTable_mouseStSt/matrix.mtx.gz
2) sc_liver_data.h5ad
3) sc_liver_data_downsample.h5ad

merging 
1) MoreDataForLogReg/liver_clustering_on_tangram_mapping/sc_genes_spatial_cell.h5ad
2) sc_genes_spatial_cell.csv 

clustering 
1) MoreDataForLogReg/liver_clustering_on_tangram_mapping/filter_genes_tangram_mapping.csv