diff --git a/.gitignore b/.gitignore
index ae480bcf828397ef961bc1f874b51633b63a9908..2f4641363ee464daa3e980c7971f8f1b36bc0abb 100755
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,6 @@
 analysis/
 *.err
-*.out
\ No newline at end of file
+*.out
+*.Rhistory
+*.Rda
+*.RData
\ No newline at end of file
diff --git a/README.md b/README.md
index a4a6cfdde2b337b1cda58826e52daa00db1c616b..146a77ac1642a781115468ccdc07b22bec91f1a9 100644
--- a/README.md
+++ b/README.md
@@ -1,11 +1,11 @@
 Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing
 ========================================================================================
 * Contact: Gervaise H. Henry
-* Email: gervaise.henry@gutsouthwestern.edu
+* Email: gervaise.henry@utsouthwestern.edu
 * Institution: UT Southwestern Medical Center
 * Department: Urology
 
-# Data Analysis
+## Data Analysis
 * Requirements:
 	* 10x CellRanger analyzed data:
 		* "filtered\_gene\_bc\_matrice_mex" folder
diff --git a/bash.scripts/sc_FullAnalysis-Pr.sh b/bash.scripts/sc_FullAnalysis-Pr.sh
index abfa320931190cd03a1faf72a39d5a2e1f8551c6..b74b0cab4acdbd404be6cc774ae76081a56d2067 100755
--- a/bash.scripts/sc_FullAnalysis-Pr.sh
+++ b/bash.scripts/sc_FullAnalysis-Pr.sh
@@ -30,7 +30,7 @@
 #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
 
 # COMMAND GROUP 1
 Rscript ../r.scripts/sc_Demultiplex.R
diff --git a/r.scripts/sc_Cluster.R b/r.scripts/sc_Cluster.R
index b5d2ff816ec64f83a2a45b020b4f077c7de54c35..3eb76eb6439e976e837d85582ee0de1383503c99 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 9333b150be41bf1062f8f5c532a7f51caa3c547f..7094ff7181bc6a5731464bb600f5ac74e3333b1b 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 c9dfcb4258a4435cc885268015c78535fc5a3e03..593aca6c76cb778af73a7573006c25882fbe5c3a 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_PC.Score.NE.R b/r.scripts/sc_PC.Score.NE.R
index 2176e1de743068041a3ca48daf09f038aab35f79..de94acbcc9d7f6608497ba47a300e443ff8543f2 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 40629aa9ac7d2c3fd1a7a5aaa5037e3ffbb975c2..0e2dae874c3071103f6e4d43c031f6897d3de5a9 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 a7acbed7a7bc799c1c7be9825c17b369dae844af..68689da0f1c13635e9aee50b52d6c620704282a5 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.Epi.R b/r.scripts/sc_QuSAGE.Epi.R
index d93b26b6a50369da731741666e78a47ab5bd2f92..a0270fbde7255a1396573b64b39a1f64218c10c0 100755
--- a/r.scripts/sc_QuSAGE.Epi.R
+++ b/r.scripts/sc_QuSAGE.Epi.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.LGEA.Epi.R b/r.scripts/sc_QuSAGE.LGEA.Epi.R
index dc595a801395ccdbbdedda152db5915d79c6a774..5d0660f933d525e40f42071ac24e3c4ef49bc649 100755
--- a/r.scripts/sc_QuSAGE.LGEA.Epi.R
+++ b/r.scripts/sc_QuSAGE.LGEA.Epi.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.LGEA.St.R b/r.scripts/sc_QuSAGE.LGEA.St.R
index f684d6ad548ac67997c259fce3e8ea32ac72a6fa..615f53b326591c376bf4f69380c7cafac776a231 100755
--- a/r.scripts/sc_QuSAGE.LGEA.St.R
+++ b/r.scripts/sc_QuSAGE.LGEA.St.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 5bcb1cb7b903bfe80b217f96dda42377ef725d78..3ef0770fe220e359a31b78a33945709d1c5b2660 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.St.R b/r.scripts/sc_QuSAGE.St.R
index 6932444e149965a4c04cf13bb2ad36c4ccde3614..8377620c26178d55e8bb0399d471a475701e4cba 100755
--- a/r.scripts/sc_QuSAGE.St.R
+++ b/r.scripts/sc_QuSAGE.St.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)
diff --git a/r.scripts/sc_Seurat.Score.CellCycle.R b/r.scripts/sc_Seurat.Score.CellCycle.R
index 628e30f8ba33b0d748da6df114bdf21cb97e8a5c..d1d06767222b6ab31cc432730244ce015d63dc5c 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 02672290926c9909b9f600d96a38022f273a97b8..0964814994aad8a09b1d2b92c12bbd88c39ab162 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)
 
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)