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@peicai peicai released this 10 Jan 22:14
· 2 commits to main since this release
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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.
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