Merge branch 'master' into test.CNV_branch

.gitignore

 analysis/
 *.err
-*.out
\ No newline at end of file
+*.out
+*.Rhistory
+*.Rda
+*.RData
\ No newline at end of file

README.md

 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

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

r.scripts/sc_Cluster.R

 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)

r.scripts/sc_D-SampleReorder.R

 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)
 

r.scripts/sc_DEG.R

 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)
 

r.scripts/sc_Demultiplex.R

 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)

r.scripts/sc_PC.Score.NE.R

 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)

r.scripts/sc_PC.Score.Stress.R

 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)

r.scripts/sc_QC.R

 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)

r.scripts/sc_QuSAGE.Epi.R

 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)

r.scripts/sc_QuSAGE.LGEA.Epi.R

 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)

r.scripts/sc_QuSAGE.LGEA.St.R

 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)

r.scripts/sc_QuSAGE.Lineage.R

 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)

r.scripts/sc_QuSAGE.St.R

-.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)

r.scripts/sc_Seurat.Score.CellCycle.R

 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)

r.scripts/sc_Tables.R

 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)
 

r.scripts/sc_mkGSEA.R

-.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)