eSpatial: a computational framework to decode the spatially divergent combinations of enhancers

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Introduction:

eSpatial is a computational framework to decode gene expression regulation by the spatially divergent combinations of enhancers through integrating spatial profiling of gene expression and chromatin accessibility.

Workflow:

Briefly, it contains the following seven steps:

Step 1. Prepare input matrix (Input)

Step 2. Reduce dimension and construct spatial neighbor network (Preprocessing)

Step 3. Detect spatial domains

Step 4. Identify spatial-specific genes and cis-regulatory elements (sGEs/sCREs)

Step 5. Define enhancer clusters of genes

Step 6. Depict spatial patterns of enhancers for genes expressed in multiple spatial domains

Step 7. Decode the combinations of spatially divergent enhancers

See tutorial for more details.