diff --git a/bash.scripts/sc_CIAnalysis-Pr.sh b/bash.scripts/sc_CIAnalysis-Pr.sh
index f402960f243a8f4060983c1036f10fc21f064dff..79d279acfb6b7f42d334f9fed0c85f1e7d5c9090 100644
--- a/bash.scripts/sc_CIAnalysis-Pr.sh
+++ b/bash.scripts/sc_CIAnalysis-Pr.sh
@@ -8,7 +8,7 @@
 #SBATCH --mail-type ALL
 #SBATCH --mail-user gervaise.henry@utsouthwestern.edu
 
-module load R/3.3.2-gccmkl
+module load R/3.4.1-gccmkl
 
 Rscript ../r.scripts/sc_Demultiplex.R
 Rscript ../r.scritps/sc_D-SampleReorder.R
diff --git a/bash.scripts/sc_FullAnalysis-Pr.sh b/bash.scripts/sc_FullAnalysis-Pr.sh
index a610938b7fbe4812ca402736df17cc8bcd1458fb..3e4c5769ed36e8f108c8ecec5bb9f2e7df71e78c 100755
--- a/bash.scripts/sc_FullAnalysis-Pr.sh
+++ b/bash.scripts/sc_FullAnalysis-Pr.sh
@@ -8,7 +8,7 @@
 #SBATCH --mail-type ALL
 #SBATCH --mail-user gervaise.henry@utsouthwestern.edu
 
-module load R/3.3.2-gccmkl
+module load R/3.4.1-gccmkl
 
 Rscript ../r.scripts/sc_Demultiplex.R
 Rscript ../r.scritps/sc_D-SampleReorder.R
diff --git a/r.scripts/sc_CI.TestData.Create.R b/r.scripts/sc_CI.TestData.Create.R
index 5b8f04f8feb4b4fae1d0fe6e3e028d69bef3687f..ed879980d93a71993227baa0b7fcb983291de2e2 100644
--- a/r.scripts/sc_CI.TestData.Create.R
+++ b/r.scripts/sc_CI.TestData.Create.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(readr)
 library(Matrix)
 library(Seurat)
@@ -44,4 +44,4 @@ if (!dir.exists("./analysis/CI.TestData.downsample/10x/filtered_gene_bc_matrices
 
 write.table(genes.sample,file="./analysis/CI.TestData.downsample/10x/filtered_gene_bc_matrices_mex/GRCh38/genes.tsv",row.names=FALSE,col.names=FALSE,append=FALSE,sep="\t",quote=FALSE)
 write.table(barcodes.sample,file="./analysis/CI.TestData.downsample/10x/filtered_gene_bc_matrices_mex/GRCh38/barcodes.tsv",row.names=FALSE,col.names=FALSE,append=FALSE,sep="\t",quote=FALSE)
-writeMM(matrix.sample,file="./analysis/CI.TestData.downsample/10x/filtered_gene_bc_matrices_mex/GRCh38/matrix.mtx")
\ No newline at end of file
+writeMM(matrix.sample,file="./analysis/CI.TestData.downsample/10x/filtered_gene_bc_matrices_mex/GRCh38/matrix.mtx")
diff --git a/r.scripts/sc_Cluster.R b/r.scripts/sc_Cluster.R
index d3b396477b91dfb867397815a2b329aff97e3adc..1b4e0ec420a79ffe7eedee9cd1b0afa16379a51e 100755
--- a/r.scripts/sc_Cluster.R
+++ b/r.scripts/sc_Cluster.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_D-SampleReorder.R b/r.scripts/sc_D-SampleReorder.R
index 6d4ed1a387ff6b54b7973295ee5331eae5662538..bbc6850ac566c7710ecc8c94c484e5012162714e 100755
--- a/r.scripts/sc_D-SampleReorder.R
+++ b/r.scripts/sc_D-SampleReorder.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_DEG.R b/r.scripts/sc_DEG.R
index 9ecc411e1d3ae9298037a071be1f0bc7dc15ac68..7e676256aab22a98e374e62efd77003f32367ce2 100755
--- a/r.scripts/sc_DEG.R
+++ b/r.scripts/sc_DEG.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_Demultiplex.R b/r.scripts/sc_Demultiplex.R
index ce453220a867daf1c8e08b74e02136271129d101..446c7fd84462458cc89ca6a797bb6e90f74e9eca 100755
--- a/r.scripts/sc_Demultiplex.R
+++ b/r.scripts/sc_Demultiplex.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_LineageSubClust.R b/r.scripts/sc_LineageSubClust.R
index c2896833c5b530790f800767224a99fd2e647a52..3ab299501be902c10e11ff1966a98c472ce5167f 100755
--- a/r.scripts/sc_LineageSubClust.R
+++ b/r.scripts/sc_LineageSubClust.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_MergeSubClust.R b/r.scripts/sc_MergeSubClust.R
index 45059fccb3ca0c2af01ac0f74e6c1d843b101f9a..1b1ed90e8ccd0ad9ae7f7ab1adf91081cc3d1c76 100755
--- a/r.scripts/sc_MergeSubClust.R
+++ b/r.scripts/sc_MergeSubClust.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 
diff --git a/r.scripts/sc_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 84789048bf3b4bb10dd5422cd8f2dfd70e69edfa..9b95a2f30d83977ca2f469732aac5cf796a8eb1f 100755
--- a/r.scripts/sc_PC.Score.NE.R
+++ b/r.scripts/sc_PC.Score.NE.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_PC.Score.Stress.R b/r.scripts/sc_PC.Score.Stress.R
index 22c5ce02a24909200250831a0f78c3266d9443ee..e6661c43f2b9294e71fcfbadeff19ae7c4446ab8 100755
--- a/r.scripts/sc_PC.Score.Stress.R
+++ b/r.scripts/sc_PC.Score.Stress.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QC.R b/r.scripts/sc_QC.R
index 103016653d5ba194b2b9593ab2338547e9bfbeac..8bfce2936d602d9302cb588798a79c6d344101c5 100755
--- a/r.scripts/sc_QC.R
+++ b/r.scripts/sc_QC.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE.Lineage.R b/r.scripts/sc_QuSAGE.Lineage.R
index c353e029f6fa092ee3478b67048a231b1c1c63b5..d017fee98b10ed8bdce3c130575057cc4a47b3ba 100755
--- a/r.scripts/sc_QuSAGE.Lineage.R
+++ b/r.scripts/sc_QuSAGE.Lineage.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE_EpiSubClust.R b/r.scripts/sc_QuSAGE_EpiSubClust.R
index 1e5546f38976e626579db915cd2d20f049e9469a..0d93b7754fff10c977b92b3610bf82b8dac93140 100755
--- a/r.scripts/sc_QuSAGE_EpiSubClust.R
+++ b/r.scripts/sc_QuSAGE_EpiSubClust.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_QuSAGE_StSubClust.R b/r.scripts/sc_QuSAGE_StSubClust.R
index 9358956022df8dde26c80dbf2dbdd0bc27751cce..ac51bced90b0f1c98a5264febe142fa47fb038a8 100755
--- a/r.scripts/sc_QuSAGE_StSubClust.R
+++ b/r.scripts/sc_QuSAGE_StSubClust.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_Seurat.Score.CellCycle.R b/r.scripts/sc_Seurat.Score.CellCycle.R
index 4cf22d50d7d43eaac96d62e3700d0ad2cea537e0..f3126ee6a0845ceab00c5c38106dbe4fe028c622 100755
--- a/r.scripts/sc_Seurat.Score.CellCycle.R
+++ b/r.scripts/sc_Seurat.Score.CellCycle.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)
diff --git a/r.scripts/sc_Tables.R b/r.scripts/sc_Tables.R
index 3ddc2c03c575b5fd449104d9227cd6cf2c68fe3a..89f81edaedc13e91e0528243c334fc0c7e18d949 100755
--- a/r.scripts/sc_Tables.R
+++ b/r.scripts/sc_Tables.R
@@ -1,5 +1,5 @@
 gc()
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 
@@ -71,4 +71,4 @@ if (opt$ne==TRUE){
   write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.SubClust.ID.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
   write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[1:4,],file=paste0("./analysis/",opt$g,"/global/table/Table.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
   write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'SubClust.ID')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
-}
\ No newline at end of file
+}
diff --git a/r.scripts/sc_mkGSEA.R b/r.scripts/sc_mkGSEA.R
index 761e87662b410375116b24ce53acc10f25e3157f..6952e4ecbf1965872d8f863c5c19a1e8ea748d3f 100755
--- a/r.scripts/sc_mkGSEA.R
+++ b/r.scripts/sc_mkGSEA.R
@@ -1,4 +1,4 @@
-.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.3")
+.libPaths("/home2/ghenry/R/x86_64-pc-linux-gnu-library/3.4")
 library(optparse)
 library(Seurat)
 library(readr)