Skip to content

diChen310/scRNA-ST_lung

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

9 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

scRNA-ST_lung

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;

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages