Function reference
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SpaCET-class
- Define the SpaCET object
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create.SpaCET.object()
- Create an SpaCET object
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create.SpaCET.object.10X()
- Create an SpaCET object from 10X Visium
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SpaCET.quality.control()
- Filter spatial spots and calculate the QC metrics
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convert.Seurat()
- Convert Seurat to SpaCET
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addTo.Seurat()
- Add SpaCET to Seurat
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SpaCET.deconvolution()
- Deconvolve tumor ST data set
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SpaCET.deconvolution.malignant()
- Deconvolve malignant cell fraction
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SpaCET.deconvolution.matched.scRNAseq()
- Deconvolve ST data set with matched scRNAseq data
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SpaCET.CCI.colocalization()
- Cell-cell colocalization analysis
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SpaCET.CCI.LRNetworkScore()
- Ligand-Receptor interaction enrichment analysis
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SpaCET.CCI.cellTypePair()
- Ligand-Receptor analysis for a co-localized cell-type pair
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SpaCET.identify.interface()
- Identify tumor-stroma interface
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SpaCET.combine.interface()
- Combine interaction spots to interface
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SpaCET.distance.to.interface()
- Distance to tumor border
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SpaCET.visualize.spatialFeature()
- Spatial feature visualization
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SpaCET.visualize.colocalization()
- Cell-cell colocalization visualization
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SpaCET.visualize.cellTypePair()
- Cell-type pair visualization
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SpaCET.GeneSetScore()
- Calculate gene set score for each spot.
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read.gmt()
- Read a gmt file.
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write.gmt()
- Write a gmt file.