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.

Update (2024.9.4)

• (1) We updated Tutorials by adding a new example(Multiple slice vs Single slice) to facilitate the reproduction of Supplementary Figure S7 in our SpaDo paper.

Update (2024.8.9)

• (1) SpaDo was originally built on Seurat 4.0.4 and SeuratObject 4.0.4. To avoid problems due to Seurat updates, We recently (2024.8.9) updated SpaDo to ensure compatibility with Seurat v5;
• (2) Enabling parallel execution for the "DistributionDistance" function when using the "JSD" distance metric, significantly reducing runtime;
• (3) We updated corresponding Tutorials.

Installation

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

  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

Contact

[email protected] or [email protected]