Updated 6 main figures

DESpace_manuscript

This repository contains the code used for the analyses presented in the manuscript “DESpace: spatially variable gene detection via differential expression testing of spatial clusters”.

Scripts in ./Analyses folder are organized as follows:

• 01_preprocessing: quality control and filtering;
• 02_run_methods: transform mouse cerebellum sce into count matrix and meta data, and run spatially variable gene detection methods in python;
• 03_simulations: generate simulated data sets and corresponding analyses in R;
• 04_multiple_samples: generate the multiple sample simulated data sets and corresponding analyses in R;
• 05_individual_clusters: obtain results for the individual cluster test;
• 06_real_data: run all SVG methods on real data in R.
• 07_varying_clusters: generate simulated data sets with varying number of clusters and corresponding analyses with DESpace.

Files in ./Figures_Tables are arranged as follows:

• Scripts contains the code to make all Figures and Tables available in the manuscript and its Supplementary;
• Figures contains all Figures shown in the manuscript and its Supplementary.

DESpace_manuscript

DESpace_manuscript

This repository contains the code used for the analyses presented in the manuscript “DESpace: spatially variable gene detection via differential expression testing of spatial clusters”.

Scripts in ./Analyses folder are organized as follows:

• 01_preprocessing: quality control and filtering;
• 02_run_methods: transform mouse cerebellum sce into count matrix and meta data, and run spatially variable gene detection methods in python;
• 03_simulations: generate simulated data sets and corresponding analyses in R;
• 04_multiple_samples: generate the multiple sample simulated data sets and corresponding analyses in R;
• 05_individual_clusters: obtain results for the individual cluster test;
• 06_real_data: run all SVG methods on real data in R.
• 07_varying_clusters: generate simulated data sets with varying number of clusters and corresponding analyses with DESpace.

Files in ./Figures_Tables are arranged as follows:

• Scripts contains the code to make all Figures and Tables available in the manuscript and its Supplementary;
• Figures contains all Figures shown in the manuscript and its Supplementary.

revision_v1

Add scran::findMarkers and seurat::FindAllMarkers

DESpace_manuscript

DESpace_manuscript

This repository contains the code used for the analyses presented in the manuscript “DESpace: spatially variable gene detection via differential expression testing of spatial clusters”.

Scripts in ./Analyses folder are organized as follows:

• 01_preprocessing: quality control and filtering;
• 02_run_methods: transform mouse cerebellum sce into count matrix and meta data, and run spatially variable gene detection methods in python;
• 03_simulations: generate simulated data sets and corresponding analyses in R;
• 04_multiple_samples: generate the multiple sample simulated data sets and corresponding analyses in R;
• 05_individual_clusters: obtain results for the individual cluster test;
• 06_real_data: run all SVG methods on real data in R.

Files in ./Figures are arranged as follows:

• Scripts contains the code to make all Figures available in the manuscript and its Supplementary;
• Figures contains all Figures shown in the manuscript and its Supplementary.

DESpace_manuscript

DESpace_manuscript

This repository contains the code used for the analyses presented in the manuscript “DESpace: spatially variable gene detection via differential expression testing of spatial clusters”.

Scripts in ./Analyses folder are organized as follows:

• 01_preprocessing: quality control and filtering;
• 02_run_methods: transform mouse cerebellum sce into count matrix and meta data, and run spatially variable gene detection methods in python;
• 03_simulations: generate simulated data sets and corresponding analyses in R;
• 04_multiple_samples: generate the multiple sample simulated data sets and corresponding analyses in R;
• 05_individual_clusters: obtain results for the individual cluster test;
• 06_real_data: run all SVG methods on real data in R.

Files in ./Figures are arranged as follows:

• Scripts contains the code to make all Figures available in the manuscript and its Supplementary;
• Figures contains all Figures shown in the manuscript and its Supplementary.