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SpaCET object

SpaCET-class
Define the SpaCET object
create.SpaCET.object()
Create an SpaCET object
create.SpaCET.object.10X()
Create an SpaCET object from 10X Visium
SpaCET.quality.control()
Filter spatial spots and calculate the QC metrics
convert.Seurat()
Convert Seurat to SpaCET
addTo.Seurat()
Add SpaCET to Seurat

Deconvolution of ST data

SpaCET.deconvolution()
Deconvolve tumor ST data set
SpaCET.deconvolution.malignant()
Deconvolve malignant cell fraction
SpaCET.deconvolution.matched.scRNAseq()
Deconvolve ST data set with matched scRNAseq data

Cell-cell interaction analysis

SpaCET.CCI.colocalization()
Cell-cell colocalization analysis
SpaCET.CCI.LRNetworkScore()
Ligand-Receptor interaction enrichment analysis
SpaCET.CCI.cellTypePair()
Ligand-Receptor analysis for a co-localized cell-type pair

Tumor-Stroma Interface

SpaCET.identify.interface()
Identify tumor-stroma interface
SpaCET.combine.interface()
Combine interaction spots to interface
SpaCET.distance.to.interface()
Distance to tumor border

Visualization

SpaCET.visualize.spatialFeature()
Spatial feature visualization
SpaCET.visualize.colocalization()
Cell-cell colocalization visualization
SpaCET.visualize.cellTypePair()
Cell-type pair visualization

Gene set score calculation

SpaCET.GeneSetScore()
Calculate gene set score for each spot.
read.gmt()
Read a gmt file.
write.gmt()
Write a gmt file.