Man pages for data2intelligence/SpaCE
Spatial Cellular Estimator for Tumors

addTo.SeuratAdd SpaCET to Seurat
convert.SeuratConvert Seurat to SpaCET
create.SpaCET.objectCreate an SpaCET object
create.SpaCET.object.10XCreate an SpaCET object from 10X Visium
read.gmtRead a gmt file
SpaCET.CCI.cellTypePairLigand-Receptor analysis for a co-localized cell-type pair
SpaCET.CCI.colocalizationCell-cell colocalization analysis
SpaCET.CCI.LRNetworkScoreLigand-Receptor interaction enrichment analysis
SpaCET-classDefine the SpaCET object
SpaCET.combine.interfaceCombine interaction spots to interface
SpaCET.deconvolutionDeconvolve tumor ST data set
SpaCET.deconvolution.malignantDeconvolve malignant cell fraction
SpaCET.deconvolution.malignant.customized.scRNAseqDeconvolve malignant fraction with customized scRNAseq data
SpaCET.deconvolution.matched.scRNAseqDeconvolve ST data set with matched scRNAseq data
SpaCET.distance.to.interfaceDistance to tumor border
SpaCET.GeneSetScoreCalculate gene set score for each spot
SpaCET.identify.interfaceIdentify tumor-stroma interface
SpaCET.quality.controlFilter spatial spots and calculate the QC metrics
SpaCET.visualize.cellTypePairCell-type pair visualization
SpaCET.visualize.colocalizationCell-cell colocalization visualization
SpaCET.visualize.spatialFeatureSpatial feature visualization
write.gmtWrite a gmt file
data2intelligence/SpaCE documentation built on Dec. 31, 2024, 5:13 a.m.