INSPIRE
v1.0.0
Instructions
Tutorials
Example 1: Analysis of human dorsolateral prefrontal cortex (DLPFC) dataset.
Example 2: Analysis of mouse brain slices with complementary views.
Example 3: Analysis of mouse brain slices across distinct ST technologies.
Example 4: Analysis of mouse whole-embryo slices across distinct ST technologies.
Example 5: Analysis of mouse whole-embryo slices across developmental stages.
Example 6: Spatial registration between two MERFISH hypothalamus sections.
Example 7: Spatial registration between two STARmap PLUS hippocampus sections.
Example 8: 3D reconstruction of mouse embryo by integrating multiple 2D slices.
Example 9: Analysis of mouse skin data undergoing wound healing
Run INSPIRE on the mouse skin sections
Analysis of spatial factors
Example 10: Analysis of human breast cancer Xenium data, revealing microenvironment heterogeneity across tumor subtypes
Installation
INSPIRE
Tutorials
Example 9: Analysis of mouse skin data undergoing wound healing
View page source
Example 9: Analysis of mouse skin data undergoing wound healing
Run INSPIRE on the mouse skin sections
Import packages
Load data
Data preprocessing
Build spaital graph
Run INSPIRE model
Access spot representations, proportions of spatial factors in spots, and gene loading matrix
Spatial distributions of spatial factors in tissues
Spot representations and spatial domain identification
Save results
Analysis of spatial factors
Load results
Visualization of gene signatures of factors
Visualization of spatial distributions of factors and their top specific genes