From bc725ac9749ac2f3a7738aa60ba3f89e52347a04 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 10 Feb 2018 22:52:54 -0600
Subject: [PATCH] Update folder references

---
 r.scripts/sc_Cluster.R                | 24 ++++++------
 r.scripts/sc_D-SampleReorder.R        | 10 ++---
 r.scripts/sc_DEG.R                    | 38 +++++++++---------
 r.scripts/sc_Demultiplex.R            | 16 ++++----
 r.scripts/sc_PC.Score.NE.R            | 46 +++++++++++-----------
 r.scripts/sc_PC.Score.Stress.R        | 46 +++++++++++-----------
 r.scripts/sc_QC.R                     | 56 +++++++++++++--------------
 r.scripts/sc_QuSAGE.Epi.R             | 40 +++++++++----------
 r.scripts/sc_QuSAGE.LGEA.Epi.R        | 40 +++++++++----------
 r.scripts/sc_QuSAGE.LGEA.St.R         | 28 +++++++-------
 r.scripts/sc_QuSAGE.Lineage.R         | 36 ++++++++---------
 r.scripts/sc_QuSAGE.St.R              | 32 +++++++--------
 r.scripts/sc_Seurat.Score.CellCycle.R | 26 ++++++-------
 r.scripts/sc_Tables.R                 | 20 +++++-----
 14 files changed, 229 insertions(+), 229 deletions(-)

diff --git a/r.scripts/sc_Cluster.R b/r.scripts/sc_Cluster.R
index 7eb7865..b5d2ff8 100755
--- a/r.scripts/sc_Cluster.R
+++ b/r.scripts/sc_Cluster.R
@@ -16,23 +16,23 @@ Project.Name <- opt$p
 PC.Max <- opt$pc
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".qc.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".qc.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".qc"))
 rm(list=paste0("sc10x.",opt$g,".qc"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
 
 #create tSNE of Sample
 sc10x.Group <- RunTSNE(object=sc10x.Group,dims.use=1:PC.Max,do.fast=TRUE)
-png(paste0("./",opt$g,"/global/tSNE_Sample.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global/tSNE_Sample.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,group.by="samples",pt.size=2.5,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -44,10 +44,10 @@ for (i  in c(5,2,1,0.5,0.2,0.1)){
   sc10x.Group <- FindClusters(object=sc10x.Group,reduction.type="pca",dims.use=1:PC.Max,resolution=i,print.output=0,save.SNN=TRUE)
   sc10x.Group <- BuildClusterTree(sc10x.Group,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
   sc10x.Group <- StashIdent(object=sc10x.Group,save.name=paste0("res",i))
-  png(paste0("./",opt$g,"/global/Tree_Global.res",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global/Tree_Global.res",i,".png"),1000,1000,pointsize=20)
   PlotClusterTree(object=sc10x.Group)
   dev.off()
-  png(paste0("./",opt$g,"/global/tSNE_Global.res",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global/tSNE_Global.res",i,".png"),1000,1000,pointsize=20)
   plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
   plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -67,6 +67,6 @@ opt.cluster <- opt
 rm(opt)
 
 #save cluser.Rda file,Cumulative.RData file
-save(list=paste0("sc10x.",opt.cluster$g,".cluster"),file=paste0("./sc10x.",Project.Name,".",opt.cluster$g,".cluster.Rda"))
+save(list=paste0("sc10x.",opt.cluster$g,".cluster"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.cluster$g,".cluster.Rda"))
 rm(list=paste0("sc10x.",opt.cluster$g,".cluster"))
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_D-SampleReorder.R b/r.scripts/sc_D-SampleReorder.R
index c7b0b12..6d4ed1a 100755
--- a/r.scripts/sc_D-SampleReorder.R
+++ b/r.scripts/sc_D-SampleReorder.R
@@ -13,16 +13,16 @@ rm(option_list)
 Project.Name <- opt$p
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".raw.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".raw.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".raw"))
 rm(list=paste0("sc10x.",opt$g,".raw"))
-sc10x.Group <- SetAllIdent(object=sc10x.Goup,id="samples")
+sc10x.Group <- SetAllIdent(object=sc10x.Group,id="samples")
 sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt","D17PrTzF_Via","D17PrPzF_Via"))
 assign(paste0("sc10x.",opt$g,".raw"),sc10x.Group)
 rm(sc10x.Group)
 
 #resave Rda file
-save(list=paste0("sc10x.",opt$g,".raw"),file=paste0("./sc10x.",Project.Name,".",opt$g,".raw.Rda"))
+save(list=paste0("sc10x.",opt$g,".raw"),file=paste0("./analysis/sc10x.",Project.Name,".",opt$g,".raw.Rda"))
 rm(list=paste0("sc10x.",opt$g,".raw"))
-rm(opt)
\ No newline at end of file
+rm(opt)
diff --git a/r.scripts/sc_DEG.R b/r.scripts/sc_DEG.R
index 74443e2..9333b15 100755
--- a/r.scripts/sc_DEG.R
+++ b/r.scripts/sc_DEG.R
@@ -21,24 +21,24 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
 sc10x.Group.NoStress <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster.IDStress.Rda"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster.IDStress.Rda"))
 sc10x.Group.Stress <- get(paste0("sc10x.",opt$g,".cluster.IDStress"))
 rm(list=paste0("sc10x.",opt$g,".cluster.IDStress"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global/DEG"))){
-  dir.create(paste0("./",opt$g,"/global/DEG"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global/DEG"))){
+  dir.create(paste0("./analysis/",opt$g,"/global/DEG"))
 }
 
 DEG.Stress <- FindMarkers(object=sc10x.Group.Stress,ident.1="Stress",ident.2="ALL",min.pct=0.5,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(5))
@@ -80,33 +80,33 @@ DEG.SM2.vs.SM1 <- DEG.SM2.vs.SM1[DEG.SM2.vs.SM1$p_val_adj<0.05,]
 
 sc10x.Group.NoStress <- SetAllIdent(object=sc10x.Group.NoStress,id="ALLSubPop")
 for (i in ls(pattern="^DEG")[!(ls(pattern="^DEG") %in% c("DEG.NE.vs.Epi","DEG.Stress"))]){
-  png(paste0("./",opt$g,"/global/DEG/Heatmap.",i,".png"),1000,1000,pointsize=20,type="quartz",antialias="none",family="Arial")
+  png(paste0("./analysis/",opt$g,"/global/DEG/Heatmap.",i,".png"),1000,1000,pointsize=20,type="quartz",antialias="none",family="Arial")
   plot(DoHeatmap(sc10x.Group.NoStress,genes.use=row.names(get(i)),slim.col.label=TRUE,group.label.rot=FALSE,group.spacing=0.5,group.order=c("BE","LE","OE","SM1","SM2","Endo"),cex.row=10,group.cex=25))
   dev.off()
 }
-png(paste0("./",opt$g,"/global/DEG/Heatmap.DEG.Stress.png"),1000,1000,pointsize=20,type="quartz",antialias="none",family="Arial")
+png(paste0("./analysis/",opt$g,"/global/DEG/Heatmap.DEG.Stress.png"),1000,1000,pointsize=20,type="quartz",antialias="none",family="Arial")
 plot(DoHeatmap(sc10x.Group.Stress,genes.use=row.names(DEG.Stress),slim.col.label=TRUE,group.label.rot=FALSE,group.spacing=0.5,group.order=c("Stress","ALL"),cex.row=10,group.cex=25))
 dev.off()
 
 sc10x.Group.NoStress <- SetAllIdent(object=sc10x.Group.NoStress,id="ALLSubPop+NE")
 for (i in ls(pattern="^DEG")[!(ls(pattern="^DEG") %in% c("DEG.Stress"))]){
-  png(paste0("./",opt$g,"/global/DEG/Violin.",i,".png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
+  png(paste0("./analysis/",opt$g,"/global/DEG/Violin.",i,".png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
   plot(VlnPlot(sc10x.Group.NoStress,features.plot=row.names(get(i))[1:10],nCol=5))
   dev.off()
-  png(paste0("./",opt$g,"/global/DEG/Ridge.",i,".png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
+  png(paste0("./analysis/",opt$g,"/global/DEG/Ridge.",i,".png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
   plot(RidgePlot(sc10x.Group.NoStress,features.plot=row.names(get(i))[1:10],nCol=5))
   dev.off()
 }
-png(paste0("./",opt$g,"/global/DEG/Violin.DEG.Stress.png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
+png(paste0("./analysis/",opt$g,"/global/DEG/Violin.DEG.Stress.png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
 plot(VlnPlot(sc10x.Group.Stress,features.plot=row.names(DEG.Stress)[1:10],nCol=5))
 dev.off()
-png(paste0("./",opt$g,"/global/DEG/Ridge.DEG.Stress.png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
+png(paste0("./analysis/",opt$g,"/global/DEG/Ridge.DEG.Stress.png"),1000,1000,pointsize=20,type="cairo",antialias="none",family="Arial")
 plot(RidgePlot(sc10x.Group.Stress,features.plot=row.names(DEG.Stress)[1:10],nCol=5))
 dev.off()
 
 for (i in ls(pattern="^DEG")){
-  write.table(get(i),file=paste0("./",opt$g,"/global/DEG/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+  write.table(get(i),file=paste0("./analysis/",opt$g,"/global/DEG/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
 }
 
-cat(row.names(DEG.Stress),file=paste0("./",opt$g,"/global/DEG/DWS.scStress.txt"),sep="\n")
-cat(row.names(DEG.NE.vs.Epi),file=paste0("./",opt$g,"/global/DEG/DWS.scNE.txt"),sep="\n")
+cat(row.names(DEG.Stress),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scStress.txt"),sep="\n")
+cat(row.names(DEG.NE.vs.Epi),file=paste0("./analysis/",opt$g,"/global/DEG/DWS.scNE.txt"),sep="\n")
diff --git a/r.scripts/sc_Demultiplex.R b/r.scripts/sc_Demultiplex.R
index 7e493d7..c9dfcb4 100755
--- a/r.scripts/sc_Demultiplex.R
+++ b/r.scripts/sc_Demultiplex.R
@@ -16,10 +16,10 @@ rm(option_list)
 Project.Name <- opt$p
 
 #load 10x data and map library_id to samples identity... initial QC min.cells/min.genes loaded based on command line options (default=3/200)
-setwd(paste0("./",Project.Name))
-sc10x.data <- Read10X(data.dir="./10x/filtered_gene_bc_matrices_mex/GRCh38/")
+setwd("../")
+sc10x.data <- Read10X(data.dir="./analysis/DATA/10x/filtered_gene_bc_matrices_mex/GRCh38/")
 sc10x <- new("seurat",raw.data=sc10x.data)
-sc10x.aggr <- read_csv(paste0("./10x/",Project.Name,"-aggr.csv"))
+sc10x.aggr <- read_csv(paste0("./analysis/DATA/10x/",Project.Name,"-aggr.csv"))
 cell.codes <- as.data.frame(sc10x@raw.data@Dimnames[[2]])
 colnames(cell.codes) <- "barcodes"
 rownames(cell.codes) <- cell.codes$barcodes
@@ -31,8 +31,8 @@ rm(cell.codes)
 rm(sc10x.aggr)
 
 #map sample categories based on demultiplex.csv and the command line option defined number of categories and save raw.Rda's for each category
-sc10x.demultiplex <- read_csv(paste0("./",Project.Name,"-demultiplex.csv"))
-Group.List <- c("ALL","samples",colnames(sc10x.demultiplex[,2:(opt$d+1)]))
+sc10x.demultiplex <- read_csv(paste0("./analysis/DATA/",Project.Name,"-demultiplex.csv"))
+Group.List <- c("samples",colnames(sc10x.demultiplex[,2:(opt$d+1)]))
 for (i in 2:(opt$d+1)){
   sc10x <- SetAllIdent(object=sc10x,id="samples")
   merge.cluster <- apply(sc10x.demultiplex[,i],1,as.character)
@@ -40,7 +40,7 @@ for (i in 2:(opt$d+1)){
   sc10x@ident <- plyr::mapvalues(x=sc10x@ident,from=sc10x.demultiplex$Samples,to=merge.cluster)
   sc10x <- StashIdent(object=sc10x,save.name=colnames(sc10x.demultiplex[,i]))
   assign(paste0("sc10x.",colnames(sc10x.demultiplex[,i]),".raw"),SubsetData(object=sc10x,ident.use=colnames(sc10x.demultiplex[,i])))
-  save(list=paste0("sc10x.",colnames(sc10x.demultiplex[,i]),".raw"),file=paste0("./sc10x.",Project.Name,".",colnames(sc10x.demultiplex[,i]),".raw.Rda"))
+  save(list=paste0("sc10x.",colnames(sc10x.demultiplex[,i]),".raw"),file=paste0("./analysis/sc10x.",Project.Name,".",colnames(sc10x.demultiplex[,i]),".raw.Rda"))
   rm(list=paste0("sc10x.",colnames(sc10x.demultiplex[,i]),".raw"))
 }
 rm(sc10x.demultiplex)
@@ -52,6 +52,6 @@ opt.demultiplex <- opt
 rm(opt)
 
 #save raw.Rda file,Cumulative.RData file
-save(sc10x,file=paste0("./sc10x.",Project.Name,".raw.Rda"))
+save(sc10x,file=paste0("./analysis/sc10x.",Project.Name,".raw.Rda"))
 rm(sc10x)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 4b8827d..2176e1d 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -24,24 +24,24 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/pc-score"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/pc-score"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score"))
 }
 
 #load resolution
@@ -49,9 +49,9 @@ sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Lineage")
 
 #subset by NE genes from Table 1 of Vashchenko,Nadezda,and Per-Anders Abrahamsson. "Neuroendocrine differentiation in prostate cancer: implications for new treatment modalities." European urology 47.2 (2005): 147-155 or DWS_scNE
 if (opt$u==FALSE){
-  DEG.NE <- read_delim("../EurUrol.2005.NE.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+  DEG.NE <- read_delim("./genesets/EurUrol.2005.NE.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 } else {
-  DEG.NE <- read_delim("../DWS.scNE.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+  DEG.NE <- read_delim("./genesets/DWS.scNE.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 }
 DEG.NE <- as.list(DEG.NE)
 sc10x.Group.NE <- as.data.frame(as.matrix(sc10x.Group@data[rownames(sc10x.Group@data) %in% unlist(DEG.NE),]))
@@ -64,26 +64,26 @@ sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="NE",slot="cell
 sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="NE",slot="key",new.data="NE")
 
 #generate PCA PC1 (NE1/NE-Score) and PC2 (NE2) and histogram of NE-Scores
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.ALL.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.ALL.png"),1000,1000,pointsize=20)
 plot <- DimPlot(object=sc10x.Group,reduction.use="NE",pt.size=2.5,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/Hist_NE.ALL.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/Hist_NE.ALL.png"),1000,1000,pointsize=20)
 histo <- hist(GetCellEmbeddings(object=sc10x.Group,reduction.type="NE",dims.use=1),breaks=10,plot=FALSE)
 plot(histo$mids,histo$density,log="y",type="h",lwd=20,lend=2,xlab="NE Score",ylab="log10 Frequency")
 dev.off()
 
 #subset to Epi only and regenerate figures above
 sc10x.Group.Epi <- SubsetData(object=sc10x.Group,ident.use="Epi")
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.Epi.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.Epi.png"),1000,1000,pointsize=20)
 plot <- DimPlot(object=sc10x.Group.Epi,reduction.use="NE",pt.size=5,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/Hist_NE.Epi.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/Hist_NE.Epi.png"),1000,1000,pointsize=20)
 histo <- hist(GetCellEmbeddings(object=sc10x.Group.Epi,reduction.type="NE",dims.use=1),breaks=10,plot=FALSE)
 plot(histo$mids,histo$density,log="y",type="h",lwd=20,lend=2,xlab="NE Score",ylab="log10 Frequency")
 dev.off()
@@ -99,7 +99,7 @@ if (clust$size[1]>clust$size[2]){
 } else {
   sc10x.Group.Epi <- SetIdent(object=sc10x.Group.Epi,cells.use=attr(clusterCut[clusterCut==as.integer(names(clust$centers[clust$centers==min(clust$centers),]))],"names"),ident.use="NE")
 }
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.Epi.Group.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/PCS_NE.Epi.Group.png"),1000,1000,pointsize=20)
 plot <- DimPlot(object=sc10x.Group.Epi,reduction.use="NE",pt.size=2.5,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -120,7 +120,7 @@ sc10x.Group.sample <- SetAllIdent(object=sc10x.Group.sample,id="Lineage")
 sc10x.Group.sample <- SetIdent(object=sc10x.Group.sample,cells.use=clusterCut,ident.use="NE")
 
 #generate tSNE plot of subsampled cells + NE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_NE.SubSample.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_NE.SubSample.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group.sample,pt.size=5,do.label=FALSE,label.size=15,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -133,11 +133,11 @@ sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("NE","Epi","St"))
 #generate violin plot of NE gene expression
 anchors <- c("CHGA","CHGB","SYP")
 for (i in anchors){
-png(paste0("./",opt$g,"/global",sub.folder,"/pc-score","/Violin_NE.",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/pc-score","/Violin_NE.",i,".png"),1000,1000,pointsize=20)
   plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,do.return=TRUE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
   plot(plot)
-dev.off()
+  dev.off()
 }
 rm(anchors)
 
@@ -174,8 +174,8 @@ opt.ne <- opt
 rm(opt)
 
 #save full .EpiPop+NE.Rda file,Cumulative.RData files
-save(list=paste0("sc10x.",opt.ne$g,".cluster",sub.file,".IDepi+st+ne"),file=paste0("./sc10x.",Project.Name,".",opt.ne$g,".cluster",sub.file,".IDepi+st+ne.Rda"))
+save(list=paste0("sc10x.",opt.ne$g,".cluster",sub.file,".IDepi+st+ne"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.ne$g,".cluster",sub.file,".IDepi+st+ne.Rda"))
 rm(list=paste0("sc10x.",opt.ne$g,".cluster",sub.file,".IDepi+st+ne"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_PC.Score.Stress.R b/r.scripts/sc_PC.Score.Stress.R
index 1673c8a..40629aa 100755
--- a/r.scripts/sc_PC.Score.Stress.R
+++ b/r.scripts/sc_PC.Score.Stress.R
@@ -20,21 +20,21 @@ Project.Name <- opt$p
 PC.Max <- opt$pc
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".",opt$id,".Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".",opt$id,".Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".",opt$id))
 rm(list=paste0("sc10x.",opt$g,".",opt$id))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/pc-score"))){
-  dir.create(paste0("./",opt$g,"/pc-score"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/pc-score"))){
+  dir.create(paste0("./analysis/",opt$g,"/pc-score"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global/NoStress"))){
-  dir.create(paste0("./",opt$g,"/global/NoStress"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global/NoStress"))){
+  dir.create(paste0("./analysis/",opt$g,"/global/NoStress"))
 }
 
 #load resolution
@@ -42,10 +42,10 @@ sc10x.Group <- SetAllIdent(object=sc10x.Group,id="ALL")
 
 #subset by Stress genes from CHUANG_OXIDATIVE_STRESS_RESPONSE_UP or DWS_scStress
 if (opt$u==FALSE){
-  DEG.Stress <- read_csv("../DEG_C2.CGP.M10970.txt")
+  DEG.Stress <- read_csv("./genesets/DEG_C2.CGP.M10970.txt")
   DEG.Stress <- DEG.Stress[-1,]
 } else {
-  DEG.Stress <- read_delim("../DWS.scStress.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+  DEG.Stress <- read_delim("./genesets/DWS.scStress.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 }
 DEG.Stress <- as.list(DEG.Stress)
 sc10x.Group.Stress <- as.data.frame(as.matrix(sc10x.Group@data[rownames(sc10x.Group@data) %in% unlist(DEG.Stress),]))
@@ -58,14 +58,14 @@ sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="Stress",slot="
 sc10x.Group <- SetDimReduction(object=sc10x.Group,reduction.type="Stress",slot="key",new.data="Stress")
 
 #generate PCA PC1 (Stress1/Stress-Score) and PC2 (Stress2) and histogram of Stress-Scores
-png(paste0("./",opt$g,"/pc-score/PCS_Stress.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/pc-score/PCS_Stress.png"),1000,1000,pointsize=20)
 plot <- DimPlot(object=sc10x.Group,reduction.use="Stress",pt.size=2.5,do.return=TRUE)
 plot <- plot+geom_density2d(color="black",bins=25,alpha=0.5)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/pc-score/Hist_Stress.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/pc-score/Hist_Stress.png"),1000,1000,pointsize=20)
 histo <- hist(GetCellEmbeddings(object=sc10x.Group,reduction.type="Stress",dims.use=1),breaks=10,plot=FALSE)
 plot(histo$mids,histo$density,log="y",type="h",lwd=20,lend=2,xlab="Stress Score",ylab="log10 Frequency")
 dev.off()
@@ -81,7 +81,7 @@ if (clust$size[1]<clust$size[2]){
 }
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="ALL")
 sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=clusterCut,ident.use="Stress")
-png(paste0("./",opt$g,"/pc-score/PCS_Stress.Group.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/pc-score/PCS_Stress.Group.png"),1000,1000,pointsize=20)
 plot <- DimPlot(object=sc10x.Group,reduction.use="Stress",pt.size=2.5,do.return=TRUE)
 plot <- plot+geom_density2d(color="black",bins=25,alpha=0.5)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
@@ -98,7 +98,7 @@ sc10x.Group.sample <- SetAllIdent(object=sc10x.Group.sample,id="ALL")
 sc10x.Group.sample <- SetIdent(object=sc10x.Group.sample,cells.use=clusterCut,ident.use="Stress")
 
 #generate tSNE plot of subsampled cells + Stress
-png(paste0("./",opt$g,"/global/tSNE_Stress.SubSample.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global/tSNE_Stress.SubSample.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group.sample,pt.size=5,do.label=FALSE,label.size=15,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -109,7 +109,7 @@ sc10x.Group <- SetIdent(object=sc10x.Group,cells.use=clusterCut,ident.use="Stres
 #generate violin plot of stres gene expression
 anchors <- c("EGR1","FOS","JUN")
 for (i in anchors){
-  png(paste0("./",opt$g,"/pc-score/Violin_Stress.",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/pc-score/Violin_Stress.",i,".png"),1000,1000,pointsize=20)
   plot <- VlnPlot(object=sc10x.Group.sample,features.plot=i,do.return=TRUE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
   plot(plot)
@@ -135,7 +135,7 @@ sc10x.Group.subset <- SubsetData(object=sc10x.Group,ident.use="ALL")
 sc10x.Group.subset <- SetAllIdent(object=sc10x.Group.subset,id=paste0("res",opt$r))
 sc10x.Group.subset <- BuildClusterTree(sc10x.Group.subset,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
 sc10x.Group.subset <- StashIdent(object=sc10x.Group.subset,save.name=paste0("res",opt$r,"-Stress"))
-png(paste0("./",opt$g,"/global/tSNE_","res",opt$r,"-NoStress.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global/tSNE_","res",opt$r,"-NoStress.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group.subset,pt.size=5,do.label=FALSE,label.size=15,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -146,7 +146,7 @@ rm(merge.cluster)
 
 #regenerate tSNEs for range of resolutions
 sc10x.Group.subset <- RunTSNE(object=sc10x.Group.subset,dims.use=1:PC.Max,do.fast=TRUE,force.recalc=TRUE)
-png(paste0("./",opt$g,"/global/NoStress/tSNE_Sample.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Sample.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group.subset,group.by="samples",pt.size=2.5,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -156,10 +156,10 @@ for (i  in c(5,2,1,0.5,0.2,0.1)){
   sc10x.Group.subset <- FindClusters(object=sc10x.Group.subset,reduction.type="pca",dims.use=1:PC.Max,resolution=i,print.output=0,save.SNN=TRUE)
   sc10x.Group.subset <- BuildClusterTree(sc10x.Group.subset,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
   sc10x.Group.subset <- StashIdent(object=sc10x.Group.subset,save.name=paste0("res",i))
-  png(paste0("./",opt$g,"/global/NoStress/Tree_Global.res",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global/NoStress/Tree_Global.res",i,".png"),1000,1000,pointsize=20)
   PlotClusterTree(object=sc10x.Group.subset)
   dev.off()
-  png(paste0("./",opt$g,"/global/NoStress/tSNE_Global.res",i,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global/NoStress/tSNE_Global.res",i,".png"),1000,1000,pointsize=20)
   plot <- TSNEPlot(object=sc10x.Group.subset,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
   plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -192,8 +192,8 @@ opt.stress <- opt
 rm(opt)
 
 #save full .EpiPop+Stress.Rda file,Cumulative.RData files
-save(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".IDStress"),file=paste0("./sc10x.",Project.Name,".",opt.stress$g,".",opt.stress$id,".IDStress.Rda"))
-save(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".NOStress"),file=paste0("./sc10x.",Project.Name,".",opt.stress$g,".",opt.stress$id,".NOStress.Rda"))
+save(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".IDStress"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.stress$g,".",opt.stress$id,".IDStress.Rda"))
+save(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".NOStress"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.stress$g,".",opt.stress$id,".NOStress.Rda"))
 rm(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".IDStress"))
 rm(list=paste0("sc10x.",opt.stress$g,".",opt.stress$id,".NOStress"))
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QC.R b/r.scripts/sc_QC.R
index a4294fd..a7acbed 100755
--- a/r.scripts/sc_QC.R
+++ b/r.scripts/sc_QC.R
@@ -22,24 +22,24 @@ rm(option_list)
 Project.Name <- opt$p
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
 if (opt$cc==TRUE){
-  load(paste0("./sc10x.",Project.Name,".",opt$g,".cc.Rda"))
+  load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cc.Rda"))
   sc10x.Group <- get(paste0("sc10x.",opt$g,".cc"))
   rm(list=paste0("sc10x.",opt$g,".cc"))
 } else {
-  load(paste0("./sc10x.",Project.Name,".",opt$g,".raw.Rda"))
+  load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".raw.Rda"))
   sc10x.Group <- get(paste0("sc10x.",opt$g,".raw"))
   rm(list=paste0("sc10x.",opt$g,".raw"))
 }
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/qc"))){
-  dir.create(paste0("./",opt$g,"/qc"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/qc"))){
+  dir.create(paste0("./analysis/",opt$g,"/qc"))
 }
 
 #filter cells
@@ -47,11 +47,11 @@ mito.genes <- grep(pattern="^MT-",x=rownames(x=sc10x.Group@data),value=TRUE)
 percent.mito <- colSums(sc10x.Group@raw.data[mito.genes,])/colSums(sc10x.Group@raw.data)
 sc10x.Group <- AddMetaData(object=sc10x.Group,metadata=percent.mito,col.name="percent.mito")
 sc10x.Group <- SetAllIdent(object=sc10x.Group,id="ALL")
-png(paste0("./",opt$g,"/qc/Violin_qc.raw.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Violin_qc.raw.png"),1000,1000,pointsize=20)
 plot <- VlnPlot(object=sc10x.Group,features.plot=c("nGene","nUMI","percent.mito"),nCol=3,do.return=TRUE)
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_qc.raw.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_qc.raw.png"),1000,1000,pointsize=20)
 par(mfrow=c(1,2))
 GenePlot(object=sc10x.Group,gene1="nUMI",gene2="percent.mito")
 GenePlot(object=sc10x.Group,gene1="nUMI",gene2="nGene")
@@ -60,11 +60,11 @@ sc10x.Group.RawCellCount <- length(sc10x.Group@data@Dimnames[[2]])
 sc10x.Group.RawGeneCount <- length(sc10x.Group@data@Dimnames[[1]])
 sc10x.Group <- FilterCells(object=sc10x.Group,subset.names=c("nGene","percent.mito"),low.thresholds=c(opt$lg,opt$lm),high.thresholds=c(opt$hg,opt$hm))
 sc10x.Group <- NormalizeData(object=sc10x.Group,normalization.method="LogNormalize",scale.factor=10000)
-png(paste0("./",opt$g,"/qc/Violin_qc.filtered.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Violin_qc.filtered.png"),1000,1000,pointsize=20)
 plot <- VlnPlot(object=sc10x.Group,features.plot=c("nGene","nUMI","percent.mito"),nCol=3,do.return=TRUE)
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_qc.filtered.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_qc.filtered.png"),1000,1000,pointsize=20)
 par(mfrow=c(1,2))
 GenePlot(object=sc10x.Group,gene1="nUMI",gene2="percent.mito")
 GenePlot(object=sc10x.Group,gene1="nUMI",gene2="nGene")
@@ -79,7 +79,7 @@ if (opt$cc==TRUE){
   gc()
   sc10x.Group <- RunPCA(object=sc10x.Group,pc.genes=c(s.genes,g2m.genes),do.print=FALSE,pcs.store=2)
   sc10x.Group <- SetAllIdent(object=sc10x.Group,id="Phase")
-  png(paste0("./",opt$g,"/cc/PCA_cc.Norm.png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/cc/PCA_cc.Norm.png"),1000,1000,pointsize=20)
   plot <- PCAPlot(object=sc10x.Group,do.return=TRUE)
   plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
   plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -97,45 +97,45 @@ rm(mito.genes)
 rm(percent.mito)
 
 #generate qc figures
-png(paste0("./",opt$g,"/qc/Plot_PCElbow.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_PCElbow.png"),1000,1000,pointsize=20)
 plot <- PCElbowPlot(object=sc10x.Group,num.pc=50)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20))
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.01.09.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.01.09.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=1:9)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.10.18.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.10.18.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=10:18)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.19.27.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.19.27.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=19:27)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.28.36.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.28.36.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=28:36)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.37.45.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.37.45.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=37:45)
 dev.off()
-png(paste0("./",opt$g,"/qc/Plot_VizPCA.46.50.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Plot_VizPCA.46.50.png"),1000,1000,pointsize=20)
 VizPCA(object=sc10x.Group,pcs.use=46:50)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.01.09.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.01.09.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=1:9,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.10.18.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.10.18.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=10:18,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.19.27.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.19.27.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=19:27,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.28.36.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.28.36.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=28:36,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.37.45.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.37.45.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=37:45,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
-png(paste0("./",opt$g,"/qc/Heatmap_PC.46.50.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/qc/Heatmap_PC.46.50.png"),1000,1000,pointsize=20)
 PCHeatmap(object=sc10x.Group,pc.use=46:50,cells.use=500,do.balanced=TRUE,label.columns=FALSE,use.full=FALSE)
 dev.off()
 
@@ -157,6 +157,6 @@ opt.qc <- opt
 rm(opt)
 
 #save qc.Rda file,Cumulative.RData file
-save(list=paste0("sc10x.",opt.qc$g,".qc"),file=paste0("./sc10x.",Project.Name,".",opt.qc$g,".qc.Rda"))
+save(list=paste0("sc10x.",opt.qc$g,".qc"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.qc$g,".qc.Rda"))
 rm(list=paste0("sc10x.",opt.qc$g,".qc"))
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QuSAGE.Epi.R b/r.scripts/sc_QuSAGE.Epi.R
index f62fd25..d93b26b 100755
--- a/r.scripts/sc_QuSAGE.Epi.R
+++ b/r.scripts/sc_QuSAGE.Epi.R
@@ -25,24 +25,24 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDlineage.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDlineage.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDlineage"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDlineage"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/correlation"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/correlation"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))
 }
 
 #load resolution
@@ -78,15 +78,15 @@ for (i in 1:Number.Clusters){
   cC[i] <- paste0("Cluster_",i,"-REST")
 }
 rm(labels)
-gene.set2 <- read_delim("../DEG_BE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_BE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "BE"
 gene.set <- c(gene.set2)
-gene.set2 <- read_delim("../DEG_LE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_LE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "LE"
 gene.set <- c(gene.set,gene.set2)
-gene.set2 <- read_delim("../DEG_OE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_OE_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "OE"
 gene.set <- c(gene.set,gene.set2)
@@ -140,7 +140,7 @@ for (j in 1:3){
   } else if (j==3) {
     pop <- "OE"
   }
-  png(paste0("./",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in Epi){
     qs <- get(paste0("qs.results.",i))
     if (i==Epi[1]){
@@ -170,7 +170,7 @@ sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("BE","LE","OE","St"))
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="EpiPop")
 
 #generate EpiPop tSNE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_EpiPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_EpiPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -255,7 +255,7 @@ rm(BE)
 rm(LE)
 rm(OE)
 rm(merge.cluster)
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_EpiSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./anaysis/",opt$g,"/global",sub.folder,"/tSNE_EpiSubPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -285,10 +285,10 @@ opt.epipop <- opt
 rm(opt)
 
 #save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.EpiPop.Rda"))
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.EpiPop.Rda"))
 rm(list=ls(pattern="^qs."))
-save(list=paste0("sc10x.",opt.epipop$g,".cluster",sub.file,".IDepi"),file=paste0("./sc10x.",Project.Name,".",opt.epipop$g,".cluster",sub.file,".IDepi.Rda"))
+save(list=paste0("sc10x.",opt.epipop$g,".cluster",sub.file,".IDepi"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.epipop$g,".cluster",sub.file,".IDepi.Rda"))
 rm(list=paste0("sc10x.",opt.epipop$g,".cluster",sub.file,".IDepi"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QuSAGE.LGEA.Epi.R b/r.scripts/sc_QuSAGE.LGEA.Epi.R
index 382ff61..dc595a8 100755
--- a/r.scripts/sc_QuSAGE.LGEA.Epi.R
+++ b/r.scripts/sc_QuSAGE.LGEA.Epi.R
@@ -26,24 +26,24 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/correlation"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/correlation"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))
 }
 
 #load resolution
@@ -79,17 +79,17 @@ for (i in 1:Number.Clusters){
   cC[i] <- paste0("Cluster_",i,"-REST")
 }
 rm(labels)
-gene.set2 <- read_csv("../Basal cells-signature-genes.csv")
+gene.set2 <- read_csv("./genesets/Basal cells-signature-genes.csv")
 gene.set2 <- gene.set2[,2]
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "hBC"
 gene.set <- c(gene.set2)
-gene.set2 <- read_csv("../Normal AT2 cells-signature-genes.csv")
+gene.set2 <- read_csv("./genesets/Normal AT2 cells-signature-genes.csv")
 gene.set2 <- gene.set2[,2]
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "hAT2"
 gene.set <- c(gene.set,gene.set2)
-gene.set2 <- read_csv("../Club_Goblet cells-signature-genes.csv")
+gene.set2 <- read_csv("./genesets/Club_Goblet cells-signature-genes.csv")
 gene.set2 <- gene.set2[,2]
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "hCGC"
@@ -144,7 +144,7 @@ for (j in 1:3){
   } else if (j==3) {
     pop <- "hCGC"
   }
-  png(paste0("./",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./genesets/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in Epi){
     qs <- get(paste0("qs.results.",i))
     if (i==Epi[1]){
@@ -177,7 +177,7 @@ sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=Epi,to=merge.clust
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="LGEA.Epi")
 
 #generate EpiPop tSNE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_LGEA.Epi.png"),1000,1000,pointsize=20)
+png(paste0("./genesets/",opt$g,"/global",sub.folder,"/tSNE_LGEA.Epi.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -256,7 +256,7 @@ for (i in 1:Number.Clusters){
         }}}}}
 sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=1:Number.Clusters,to=merge.cluster)
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="LGEA.EpiSubPop")
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_LGEA.EpiSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./genesets/",opt$g,"/global",sub.folder,"/tSNE_LGEA.EpiSubPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -293,10 +293,10 @@ opt.lgeaepipop <- opt
 rm(opt)
 
 #save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.LGEA.EpiPop.Rda"))
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.LGEA.EpiPop.Rda"))
 rm(list=ls(pattern="^qs."))
-save(list=paste0("sc10x.",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi"),file=paste0("./sc10x.",Project.Name,".",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi.Rda"))
+save(list=paste0("sc10x.",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi.Rda"))
 rm(list=paste0("sc10x.",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QuSAGE.LGEA.St.R b/r.scripts/sc_QuSAGE.LGEA.St.R
index 9bb38f9..f684d6a 100755
--- a/r.scripts/sc_QuSAGE.LGEA.St.R
+++ b/r.scripts/sc_QuSAGE.LGEA.St.R
@@ -26,18 +26,18 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./anaysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/correlation"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/correlation"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))
 }
 
 #load resolution
@@ -78,7 +78,7 @@ for (i in 1:Number.Clusters){
   cC[i] <- paste0("Cluster_",i,"-REST")
 }
 rm(labels)
-gene.set3 <- read_excel("../journal.pcbi.1004575.s026.XLSX",skip=2)
+gene.set3 <- read_excel("./genesets/journal.pcbi.1004575.s026.XLSX",skip=2)
 gene.set3 <- gene.set3[,c(3,9)]
 gene.set2 <- gene.set3[gene.set3$`CELL TYPE`=="C1 : Proliferative Fibroblast",]
 gene.set2 <- as.list(gene.set2[!(is.na(gene.set2$`hu Gene Symbol`)),1])
@@ -161,7 +161,7 @@ for (j in 1:6){
   } else if (j==6) {
     pop <- "MylImm"
   }
-  png(paste0("./",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in St){
     qs <- get(paste0("qs.results.",i))
     if (i==St[1]){
@@ -209,7 +209,7 @@ rm(MylImm.cells)
 rm(UK.cells)
 
 #generate LGEA StPops tSNE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_LGEA.St.png"),1000,1000,pointsize=20)
+png(paste0("./"analysis/,opt$g,"/global",sub.folder,"/tSNE_LGEA.St.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -327,7 +327,7 @@ for (i in 1:Number.Clusters){
         }}}}}
 sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=1:Number.Clusters,to=merge.cluster)
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="LGES.StSubPop")
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_LGES.StSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_LGES.StSubPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -364,10 +364,10 @@ opt.lgeastpop <- opt
 rm(opt)
 
 #save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.LGEA.StPop.Rda"))
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.LGEA.StPop.Rda"))
 rm(list=ls(pattern="^qs."))
-save(list=paste0("sc10x.",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"),file=paste0("./sc10x.",Project.Name,".",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
+save(list=paste0("sc10x.",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lgeaepipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
 rm(list=paste0("sc10x.",opt.epipop$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QuSAGE.Lineage.R b/r.scripts/sc_QuSAGE.Lineage.R
index 5a2d306..5bcb1cb 100755
--- a/r.scripts/sc_QuSAGE.Lineage.R
+++ b/r.scripts/sc_QuSAGE.Lineage.R
@@ -25,24 +25,24 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global"))){
-  dir.create(paste0("./",opt$g,"/global"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global"))){
+  dir.create(paste0("./analysis/",opt$g,"/global"))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/correlation"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/correlation"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))
 }
 
 #load resolution
@@ -72,11 +72,11 @@ for (i in 1:Number.Clusters){
   cC[i] <- paste0("Cluster_",i,"-REST")
 }
 rm(labels)
-gene.set2 <- read_delim("../DEG_FMSt_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_FMSt_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "St"
 gene.set <- c(gene.set2)
-gene.set2 <- read_delim("../DEG_Epi_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set2 <- read_delim("./genesets/DEG_Epi_2FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
 gene.set2 <- as.list(gene.set2)
 names(gene.set2) <- "Epi"
 gene.set <- c(gene.set,gene.set2)
@@ -129,7 +129,7 @@ for (j in 1:2){
   } else if (j==2) {
     pop <- "Epi"
   }
-  png(paste0("./",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in 1:Number.Clusters){
     qs <- get(paste0("qs.results.",i))
     if (i==1){
@@ -156,7 +156,7 @@ sc10x.Group@ident <- factor(sc10x.Group@ident,levels=c("Epi","St"))
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="Lineage")
 
 #generate lineage tSNE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_Lineage.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_Lineage.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -183,10 +183,10 @@ opt.lineage <- opt
 rm(opt)
 
 #save QuSAGE.Lineage.Rda,IDlineage.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.Lineage.Rda"))
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.Lineage.Rda"))
 rm(list=ls(pattern="^qs."))
-save(list=paste0("sc10x.",opt.lineage$g,".cluster",sub.file,".IDlineage"),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,".cluster",sub.file,".IDlineage.Rda"))
+save(list=paste0("sc10x.",opt.lineage$g,".cluster",sub.file,".IDlineage"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,".cluster",sub.file,".IDlineage.Rda"))
 rm(list=paste0("sc10x.",opt.lineage$g,".cluster",sub.file,".IDlineage"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_QuSAGE.St.R b/r.scripts/sc_QuSAGE.St.R
index 0642644..6932444 100755
--- a/r.scripts/sc_QuSAGE.St.R
+++ b/r.scripts/sc_QuSAGE.St.R
@@ -24,18 +24,18 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/global",sub.folder,"/correlation"))){
-  dir.create(paste0("./",opt$g,"/global",sub.folder,"/correlation"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))){
+  dir.create(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation"))
 }
 
 #load resolution
@@ -71,15 +71,15 @@ for (i in 1:Number.Clusters){
   cC[i] <- paste0("Cluster_",i,"-REST")
 }
 rm(labels)
-gene.set2 <- read_delim("../DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set2 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set2 <- as.list(gene.set2[-1,])
 names(gene.set2) <- "Endo"
 gene.set <- c(gene.set2)
-gene.set2 <- read_delim("../DEG_C5.BP.M10794.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set2 <- read_delim("./genesets/DEG_C5.BP.M10794.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set2 <- as.list(gene.set2[-1,])
 names(gene.set2) <- "SM"
 gene.set <- c(gene.set,gene.set2)
-gene.set2 <- read_delim("../DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set2 <- read_delim("./genesets/DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
 gene.set2 <- as.list(gene.set2[-1,])
 names(gene.set2) <- "Fib"
 gene.set <- c(gene.set,gene.set2)
@@ -133,7 +133,7 @@ for (j in 1:3){
   } else if (j==3) {
     pop <- "Fib"
   }
-  png(paste0("./",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
+  png(paste0("./analysis/",opt$g,"/global",sub.folder,"/correlation/QuSAGE_",pop,".png"),1000,1000,pointsize=20)
   for (i in St){
     qs <- get(paste0("qs.results.",i))
     if (i==St[1]){
@@ -173,7 +173,7 @@ rm(Fib.cells)
 rm(UK.cells)
 
 #generate ALLPop tSNE
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_ALLPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_ALLPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -291,7 +291,7 @@ for (i in 1:Number.Clusters){
         }}}}}
 sc10x.Group@ident <- plyr::mapvalues(x=sc10x.Group@ident,from=1:Number.Clusters,to=merge.cluster)
 sc10x.Group <- StashIdent(object=sc10x.Group,save.name="ALLSubPop")
-png(paste0("./",opt$g,"/global",sub.folder,"/tSNE_ALLSubPop.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/global",sub.folder,"/tSNE_ALLSubPop.png"),1000,1000,pointsize=20)
 plot <- TSNEPlot(object=sc10x.Group,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -329,10 +329,10 @@ opt.stpop <- opt
 rm(opt)
 
 #save QuSAGE.EpiPop.Rda,IDepi.Rda file,Cumulative.RData files
-save(list=ls(pattern="^qs."),file=paste0("./sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.StPop.Rda"))
+save(list=ls(pattern="^qs."),file=paste0("./analysis/sc10x.",Project.Name,".",opt.lineage$g,sub.file,".QuSAGE.StPop.Rda"))
 rm(list=ls(pattern="^qs."))
-save(list=paste0("sc10x.",opt.stpop$g,".cluster",sub.file,".IDepi+st"),file=paste0("./sc10x.",Project.Name,".",opt.stpop$g,".cluster",sub.file,".IDepi+st.Rda"))
+save(list=paste0("sc10x.",opt.stpop$g,".cluster",sub.file,".IDepi+st"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.stpop$g,".cluster",sub.file,".IDepi+st.Rda"))
 rm(list=paste0("sc10x.",opt.stpop$g,".cluster",sub.file,".IDepi+st"))
 rm(sub.folder)
 rm(sub.file)
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_Seurat.Score.CellCycle.R b/r.scripts/sc_Seurat.Score.CellCycle.R
index 4e7ea82..628e30f 100755
--- a/r.scripts/sc_Seurat.Score.CellCycle.R
+++ b/r.scripts/sc_Seurat.Score.CellCycle.R
@@ -14,37 +14,37 @@ rm(option_list)
 Project.Name <- opt$p
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".raw.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".raw.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".raw"))
 rm(list=paste0("sc10x.",opt$g,".raw"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/cc"))){
-  dir.create(paste0("./",opt$g,"/cc"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/cc"))){
+  dir.create(paste0("./analysis/",opt$g,"/cc"))
 }
 
 #score cell cycle and generate figures
-cc.genes <- readLines(con="../regev_lab_cell_cycle_genes.txt")
+cc.genes <- readLines(con="./genesets/regev_lab_cell_cycle_genes.txt")
 s.genes <- cc.genes[1:43]
 g2m.genes <- cc.genes[44:97]
 sc10x.Group <- NormalizeData(object=sc10x.Group)
 sc10x.Group <- ScaleData(object=sc10x.Group)
 sc10x.Group <- CellCycleScoring(object=sc10x.Group,s.genes=s.genes,g2m.genes=g2m.genes,set.ident=TRUE)
-png(paste0("./",opt$g,"/cc/Ridge_cc.Raw.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/cc/Ridge_cc.Raw.png"),1000,1000,pointsize=20)
 plot <- RidgePlot(object=sc10x.Group,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),y.log=TRUE,nCol=2,do.return=TRUE)
 plot(plot)
 dev.off()
-png(paste0("./",opt$g,"/cc/Violin_cc.Raw.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/cc/Violin_cc.Raw.png"),1000,1000,pointsize=20)
 plot <- VlnPlot(object=sc10x.Group,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),nCol=2,do.return=TRUE)
 plot(plot)
 dev.off()
 sc10x.Group <- RunPCA(object=sc10x.Group,pc.genes=c(s.genes,g2m.genes),do.print=FALSE,pcs.store=2)
-png(paste0("./",opt$g,"/cc/PCA_cc.Raw.png"),1000,1000,pointsize=20)
+png(paste0("./analysis/",opt$g,"/cc/PCA_cc.Raw.png"),1000,1000,pointsize=20)
 plot <- PCAPlot(object=sc10x.Group,do.return=TRUE)
 plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
 plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
@@ -61,6 +61,6 @@ opt.cc <- opt
 rm(opt)
 
 #save qc.Rda file,Cumulative.RData file
-save(list=paste0("sc10x.",opt.cc$g,".cc"),file=paste0("./sc10x.",Project.Name,".",opt.cc$g,".cc.Rda"))
+save(list=paste0("sc10x.",opt.cc$g,".cc"),file=paste0("./analysis/sc10x.",Project.Name,".",opt.cc$g,".cc.Rda"))
 rm(list=paste0("sc10x.",opt.cc$g,".cc"))
-save.image(file=paste0("./sc10x.",Project.Name,".Cumulative.RData"))
+save.image(file=paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
diff --git a/r.scripts/sc_Tables.R b/r.scripts/sc_Tables.R
index d9d01e7..0267229 100755
--- a/r.scripts/sc_Tables.R
+++ b/r.scripts/sc_Tables.R
@@ -21,20 +21,20 @@ if (opt$st==TRUE){
 }
 
 #load data
-setwd(paste0("./",Project.Name))
-load(paste0("./sc10x.",Project.Name,".Cumulative.RData"))
-load(paste0("./sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
+setwd("../")
+load(paste0("./analysis/sc10x.",Project.Name,".Cumulative.RData"))
+load(paste0("./analysis/sc10x.",Project.Name,".",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst.Rda"))
 sc10x.Group <- get(paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"))
 rm(list=paste0("sc10x.",opt$g,".cluster",sub.file,".IDepi+st+ne+LGEAepi+LGEAst"))
 
 #create folder structure
-if (!dir.exists(paste0("./",opt$g))){
-  dir.create(paste0("./",opt$g))
+if (!dir.exists(paste0("./analysis/",opt$g))){
+  dir.create(paste0("./analysis/",opt$g))
 }
-if (!dir.exists(paste0("./",opt$g,"/table"))){
-  dir.create(paste0("./",opt$g,"/table"))
+if (!dir.exists(paste0("./analysis/",opt$g,"/table"))){
+  dir.create(paste0("./analysis/",opt$g,"/table"))
 }
 
-write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./",opt$g,"/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./",opt$g,"/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./",opt$g,"/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./analysis/",opt$g,"/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
+write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-- 
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