scRNA_workflow.R: The main analysis of scRNA-seq including the QC, integration, clustering, cell type definition as well as identification of the differences among multiple lesions of the same patients.
stRNA_workflow.R: The analyses based on spatial transcriptomics (ST) or integration of both scRNA-seq and ST including the QC, integration, clustering, cell type prediction based on the scRNA-seq data, and pathological sub-type analysis.
epiSubClustering.R: subtype analysis for the epithelial cells.
tCellSubClustering.R:subtype analysis for the T&NK cells.
BCellSubClustering.R:subtype analysis for the B cells.
endoCellSubClustering.R: subtype analysis for the endothelial cells.
myeloidCellSubClustering.R: subtype analysis for the myeloid cells.
inferCNV.R & inferCNVDownStreamAnalysis.R: cnv based analysis.
scDC_cellTypeCompositionDiffAnalysis: identification of cell composition differences between different samples.
compareGEOSC_GSE148071.R, compareGEOSC_GSE148466.R,compareWithGEO131907,compareTCGA.R,checkGEOForBiomarkers.R:investigate other datasets to validate the new findings.
cellChatAnalysis_cldn2.R: find cellular communications of the epithelial cells and focused on the difference of CLDN2 AT2 cells;