SpaDo

Multi-slice Spatial Transcriptome Domain Analysis.

Fig 1. Workflow of SpaDo. a. Calculating the SPACE for both single-cell resolution and spot resolution spatial transcriptomic data. SPACE: SPatially Adjacent Cell type Embedding. b. Three functions involved in multi-slice spatial domain analysis: multi-slice domain detection, reference-based spatial domain annotation, and multi-slice clustering analysis by consideration of spatial domain composition. JSD, Jensen Shannon Divergence.

Overview

With the rapid advancements in spatial transcriptome sequencing, multiple tissue slices are now available, enabling the integration and interpretation of spatial cellular landscapes. Herein, we introduce SpaDo, a tool for multi-slice spatial domain analysis, including modules for multi-slice spatial domain detection, reference-based annotation, and multiple slice clustering at both single-cell and spot resolutions. We demonstrate SpaDo's effectiveness with over 40 multi-slice spatial transcriptome datasets from 7 sequencing platforms. Our findings highlight SpaDo's potential to reveal novel biological insights in multi-slice spatial transcriptomes.

Installation

• SpaDo package can be installed from Github using devtools packages with R>=4.0.5.

• Attention： SpaDo was originally built on Seurat 4.0.4 and SeuratObject 4.0.4. To avoid problems due to Seurat updates, please make sure you are using the same version of Seurat and SeuratObject packages （Seurat 4.0.4 and SeuratObject 4.0.4）!

  library(devtools)
  install_github("bm2-lab/SpaDo")

Getting started

Here are Tutorials with different styles and Demo datasets used in our tutorials.

Citation

Duan, B., Chen, S., Cheng, X. et al. Multi-slice spatial transcriptome domain analysis with SpaDo. Genome Biol 25, 73 (2024). https://doi.org/10.1186/s13059-024-03213-x