├── .gitattributes ├── .gitignore ├── Analysis ├── BMDC Pseudotime │ ├── Antiviral analysis.ipynb │ └── DE Analsysis.ipynb ├── BreastCancer │ ├── Alternative explanatory factors.ipynb │ ├── Automatic expression histology.ipynb │ ├── BC_MS_results.csv │ ├── BC_final_results.csv │ ├── BC_gProfiler.csv │ ├── BC_sample_info.csv │ ├── Breast Cancer Tissue Analysis.ipynb │ ├── Clustering analysis.ipynb │ ├── Compare to Rank-normalisation.ipynb │ ├── Spatial Shuffling.ipynb │ ├── Standard Errors.ipynb │ ├── data │ │ ├── HE_layer2_BC.jpg │ │ └── Layer2_BC_count_matrix-1.tsv │ └── spatial_BC_analysis.py ├── Comparison │ ├── Compare performance.ipynb │ ├── Snakefile │ ├── gpy_sim_comparison.py │ ├── performance.csv │ ├── run.sh │ ├── run_spatialde.py │ ├── run_stan.py │ └── simulate_data.py ├── Frog │ ├── Frog Development Analysis.ipynb │ ├── Frog_MS_results.csv │ ├── Frog_final_results.csv │ ├── Frog_sample_info.csv │ ├── data │ │ ├── GSE65785_clutchApolyA_relative_TPM.csv │ │ └── sample_info.csv │ └── temporal_Frog_analysis.py ├── HVG-analysis │ └── HVG in each dataset.ipynb ├── MERFISH │ ├── MERFISH Analysis.ipynb │ ├── Make MERFISH Expression table.ipynb │ ├── data │ │ ├── codebook.csv │ │ └── rep6 │ │ │ ├── middle_exp_mat.csv │ │ │ ├── middle_sample_info.csv │ │ │ ├── rep6-part1.csv │ │ │ ├── rep6-part10.csv │ │ │ ├── rep6-part11.csv │ │ │ ├── rep6-part12.csv │ │ │ ├── rep6-part13.csv │ │ │ ├── rep6-part14.csv │ │ │ ├── rep6-part15.csv │ │ │ ├── rep6-part16.csv │ │ │ ├── rep6-part17.csv │ │ │ ├── rep6-part18.csv │ │ │ ├── rep6-part19.csv │ │ │ ├── rep6-part2.csv │ │ │ ├── rep6-part20.csv │ │ │ ├── rep6-part3.csv │ │ │ ├── rep6-part4.csv │ │ │ ├── rep6-part5.csv │ │ │ ├── rep6-part6.csv │ │ │ ├── rep6-part7.csv │ │ │ ├── rep6-part8.csv │ │ │ └── rep6-part9.csv │ ├── middle_MS_results.csv │ ├── middle_final_results.csv │ ├── middle_sample_info.csv │ └── spatial_MERFISH_analysis.py ├── MouseOB │ ├── AEH prototyping.ipynb │ ├── AEH_times.csv │ ├── Automatic expression histology.ipynb │ ├── Clustering analysis.ipynb │ ├── Compare clustering and AEH.ipynb │ ├── MOB_MS_results.csv │ ├── MOB_clustering.csv │ ├── MOB_clusters.pdf │ ├── MOB_final_results.csv │ ├── MOB_sample_info.csv │ ├── MOB_significance_comparison.pdf │ ├── Mouse Olfactory Bulb Analysis.ipynb │ ├── PCA_MOB.pdf │ ├── Periodic vs SE.ipynb │ ├── Variational inference.ipynb │ ├── data │ │ ├── HE_Rep11_MOB.jpg │ │ ├── Rep11_MOB_0.csv │ │ ├── Rep12_MOB_0.csv │ │ └── split_data.py │ ├── mob-gmm-weights.pdf │ ├── spatial_MOB_analysis.py │ └── time_AEH.py ├── SeqFISH │ ├── Automatic expression histology.ipynb │ ├── Extract SeqFISH count matrices.ipynb │ ├── MS_results_43.csv │ ├── Periodic vs linear.ipynb │ ├── SeqFISH Analysis.ipynb │ ├── SeqFISH Results.ipynb │ ├── exp_mat_43.csv │ ├── final_results_43.csv │ ├── mmc6.xlsx │ ├── sample_info_43.csv │ └── spatial_SeqFISH_analysis.py ├── Theory │ ├── 3d-grid.pdf │ ├── 3d-line.pdf │ ├── 3d-pionts.pdf │ ├── 3d-points.pdf │ ├── 3d-surface.pdf │ ├── 3d.pdf │ ├── AEH timing.ipynb │ ├── Anscombe transformation.ipynb │ ├── Bootstraps │ │ ├── Investigate Robustness.ipynb │ │ ├── Snakefile │ │ └── bootstraps_CB_analysis.py │ ├── Covariance illustration.ipynb │ ├── Example Spatial Patterns.ipynb │ ├── P-value estimation.ipynb │ ├── Periods and length scales.ipynb │ ├── Simulation from basis function.ipynb │ ├── Simulation from model.ipynb │ ├── Simulation from null model.ipynb │ └── make_BC_null_simulations.py └── rerun_all.sh ├── LICENSE ├── Python-module ├── README.rst ├── SpatialDE │ ├── __init__.py │ ├── aeh.py │ ├── aha.py │ ├── anndata.py │ ├── base.py │ ├── plot.py │ ├── scripts │ │ ├── __init__.py │ │ └── spatialde_cli.py │ └── util.py ├── setup.cfg └── setup.py ├── R-package └── SpatialDE │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ └── base.R │ ├── SpatialDE.Rproj │ └── scripts │ └── example.R ├── README.ipynb ├── README.rst ├── README_files ├── README_16_0.png ├── README_17_0.png ├── README_19_0.png ├── 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