From 91f3a49e345e666e88b4d460ff23675ddb66e63b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 20 Apr 2018 10:53:18 -0500
Subject: [PATCH] Upgrade to R/3.4.1

---
 bash.scripts/sc_CIAnalysis-Pr.sh      | 2 +-
 bash.scripts/sc_FullAnalysis-Pr.sh    | 2 +-
 r.scripts/sc_CI.TestData.Create.R     | 4 ++--
 r.scripts/sc_Cluster.R                | 2 +-
 r.scripts/sc_D-SampleReorder.R        | 2 +-
 r.scripts/sc_DEG.R                    | 2 +-
 r.scripts/sc_Demultiplex.R            | 2 +-
 r.scripts/sc_LineageSubClust.R        | 2 +-
 r.scripts/sc_MergeSubClust.R          | 2 +-
 r.scripts/sc_PC.Score.NE.R            | 2 +-
 r.scripts/sc_PC.Score.Stress.R        | 2 +-
 r.scripts/sc_QC.R                     | 2 +-
 r.scripts/sc_QuSAGE.Lineage.R         | 2 +-
 r.scripts/sc_QuSAGE_EpiSubClust.R     | 2 +-
 r.scripts/sc_QuSAGE_StSubClust.R      | 2 +-
 r.scripts/sc_Seurat.Score.CellCycle.R | 2 +-
 r.scripts/sc_Tables.R                 | 4 ++--
 r.scripts/sc_mkGSEA.R                 | 2 +-
 18 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/bash.scripts/sc_CIAnalysis-Pr.sh b/bash.scripts/sc_CIAnalysis-Pr.sh
index f402960..79d279a 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 a610938..3e4c576 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 5b8f04f..ed87998 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 d3b3964..1b4e0ec 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 6d4ed1a..bbc6850 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 9ecc411..7e67625 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 ce45322..446c7fd 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 c289683..3ab2995 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 45059fc..1b1ed90 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 8478904..9b95a2f 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 22c5ce0..e6661c4 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 1030166..8bfce29 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 c353e02..d017fee 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 1e5546f..0d93b77 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 9358956..ac51bce 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 4cf22d5..f3126ee 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 3ddc2c0..89f81ed 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 761e876..6952e4e 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)
-- 
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