Code to reproduce the analysis and figures in the paper Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace. The scSpace python package is located here.
The data used and/or generated in this study can be found on Google Drive.
The analysis scripts to produced scSpace results can be accessed here. For example, the script constructSimulations.R is used to generate simulated scRNA-seq and spatial transcriptomics data in benchmarking step.
We provide R Markdown files that were used to create the main figures, the results consistent with the figures can be accessed here:
- Performance of scSpace compared with other methods on simulated datasets (Figure 1)
- Validation of scSpace on human DLPFC 10x Visium data (Figure 2)
- Validation of scSpace on mouse primary visual cortex STARmap data (Figure 2)
- Validation of scSpace on human embryonic heart scRNA-seq data (Figure 3)
- Validation of scSpace on human MTG scRNA-seq data (Figure 4)
- Application of scSpace on human melanoma scRNA-seq data (Figure 5)
- Application of scSpace on human COVID-19 scRNA-seq data (Figure 6)