## ----reanalysis.RData, eval=FALSE--------------------------------------------- # library("scTensor") # load("reanalysis.RData") ## ----Reanalysis, eval=FALSE--------------------------------------------------- # library("AnnotationHub") # library("LRBaseDbi") # # # Create LRBase object # ah <- AnnotationHub() # dbfile <- query(ah, c("LRBaseDb", "Homo sapiens", "v002"))[[1]] # LRBase.Hsa.eg.db <- LRBaseDbi::LRBaseDb(dbfile) # # # Register the file pass of user's LRBase # metadata(sce)$lrbase <- dbfile(LRBase.Hsa.eg.db) # # # CCI Tensor Decomposition # cellCellDecomp(sce, ranks=c(6,5), assayNames="normcounts") # # # HTML Report # cellCellReport(sce, reducedDimNames="TSNE", assayNames="normcounts", # title="Cell-cell interaction within Germline_Male, GSE86146", # author="Koki Tsuyuzaki", html.open=TRUE, # goenrich=TRUE, meshenrich=FALSE, reactomeenrich=FALSE, # doenrich=FALSE, ncgenrich=FALSE, dgnenrich=FALSE) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()