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Strand Lab
sc-TissueMapper_Pr
Commits
8c6a9f85
Commit
8c6a9f85
authored
Feb 12, 2018
by
Gervaise Henry
🤠
Browse files
Merge branch 'master' into test.CNV_branch
parents
73892b82
072278b5
Changes
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.gitignore
View file @
8c6a9f85
analysis/
*.err
*.out
\ No newline at end of file
*.out
*.Rhistory
*.Rda
*.RData
\ No newline at end of file
README.md
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8c6a9f85
Determining cellular heterogeneity in the human prostate with single-cell RNA sequencing
========================================================================================
*
Contact: Gervaise H. Henry
*
Email: gervaise.henry@
g
utsouthwestern.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
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8c6a9f85
...
...
@@ -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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
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
View file @
8c6a9f85
.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
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8c6a9f85
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
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8c6a9f85
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
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8c6a9f85
.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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