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)