SONAR

SONAR is the algorithm of cell-type deconvolution for spatial transcriptomics

Installation

library(devtools)

devtools:: install_github("lzygenomics/SONAR")

Dependence

• R version >= 4.0.5.
• R packages:
  • this.path>=0.5.1; Matrix>=1.3.4; data.table>=1.14.0; Seurat>=4.0.3; matlabr=1.5.2; R.matlab=3.7.0
• MATLAB version >= R2019a
  • Just install the MATLAB, subsequent operations do not require you to use the MATLAB language

Run SONAR

1. Install the dependence

2. Install SONAR

3. Download the SONAR files: Follow the Example/SONAR-entrance.Rmd IS ALL YOU NEED

Files Annotation

• /inst/extdata/

  These files store the required input information, See SONAR-entrance.Rmd for specific format requirements.

• /result/

  These files store the output results.

  Proportions of all cell types in each spot (SONAR.results.txt);

  Spatial pie plots (pie.pdf);

  Spatial distribution of specific cell types proportion (abs_prop.pdf / scaled_prop.pdf);

  Colocalization(correlation along the spatial) for pairs of cell types (colocalization.pdf).

• /core-code/

  no need to operate.

  These files store the core code, and store the preprocessed data that delivered to SONAR.

A brif Example

Please Follow the Example/SONAR-entrance.Rmd

Publication Link

https://www.nature.com/articles/s41467-023-40458-9

How to cite SONAR

Liu, Z., Wu, D., Zhai, W. et al. SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics. Nat Commun 14, 4727 (2023). https://doi.org/10.1038/s41467-023-40458-9

Thank you, and happy researching!