SpaMosaic documentation

SpaMosaic aims to integrate mosaic datasets with partially overlapping modalities to construct higher dimensional views of tissues. SpaMosaic can handle multiple serial (or non-serial) sections from the same biological tissue or sections that form a time series such as embryo development. SpaMosaic works well on various spatial-omics technologies (spatial-atac-seq, spatial-cut&tag-seq, spatial-rna-epigenomics-seq, misar-seq, visium, stereo-seq and etc.).

Overview of SpaMosaic workflow

Features and Capabilities

From the perspective of computational task, SpaMosaic can handle:

1. Integration:

   • Horizontal Integration: Integrate multiple sections sharing the same modality.

   • Vertical Integration: Integrate multiple modalities from a single section.

   • Mosaic Integration: Integrate multiple sections with different multi-modal compositions.

2. Imputation:

   • For mosaic datasets, SpaMosaic imputes missing assays for each section, facilitating a more comprehensive analysis.

Getting started with SpaMosaic

To begin using SpaMosaic, please refer to the following sections of the documentation:

• The Installation provides instructions for setting up SpaMosaic in your environment.

• The Tutorials contains examples on how to use SpaMosaic for various integration and imputation tasks.