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iyhaoo · Jun 16, 2020 · 7f3ae4a · 7f3ae4a
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diff --git a/README.rst b/README.rst
@@ -181,7 +181,7 @@ Usage
     .. __: https://github.com/iyhaoo/DISC_data_availability
 
   +------------------+------------------+------------------+------------------+------------------+----------------------+
-  |Dataset           |Raw Data          |DS Data           |FISH Data         |Bulk Data         |Cell Annotation       |
+  |Dataset           |Raw Data          |DS Data           |FISH Data         |Bulk Data         |Cell Type Annotation  |
   +==================+==================+==================+==================+==================+======================+
   |`MELANOMA`__      |`YES`__           |`0.5`__           |`YES`__           |NO                |NO                    |
   +------------------+------------------+------------------+------------------+------------------+----------------------+

diff --git a/...ata Preparation, Imputation and Computational Resource Evaluation/Running Scripts/test.sh b/...ata Preparation, Imputation and Computational Resource Evaluation/Running Scripts/test.sh
@@ -340,16 +340,91 @@ R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream
 
 
 
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+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_0/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+30 1.4 "" "retina"
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_0/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+50 1.4 "" "retina"
+
+
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+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_1/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+30 1.4 "" "retina"
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_1/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+50 1.4 "" "retina"
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+CUDA_VISIBLE_DEVICES=2 HDF5_USE_FILE_LOCKING=FALSE disc \
+--dataset=/home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/raw.loom \
+--out-dir=/home/yuanhao/DISC_imputation_result/RETINA_1.1.1_2 \
+--min-expressed-cell=49 \
+--library-size-factor=median
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_2/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+30 1.4 "" "retina"
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_2/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+50 1.4 "" "retina"
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 CUDA_VISIBLE_DEVICES=3 HDF5_USE_FILE_LOCKING=FALSE disc \
 --dataset=/home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/raw.loom \
---out-dir=/home/yuanhao/DISC_imputation_result/RETINA_1.1.0_5 \
+--out-dir=/home/yuanhao/DISC_imputation_result/RETINA_1.1.1_3 \
 --min-expressed-cell=49 \
 --library-size-factor=median
 
 R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
---args /home/yuanhao/DISC_imputation_result/RETINA_1.1.0_5/result/imputation.loom \
-"" \
-/home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_3/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
 30 1.4 "" "retina"
 
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_3/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+50 1.4 "" "retina"
+
+
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+CUDA_VISIBLE_DEVICES=4 HDF5_USE_FILE_LOCKING=FALSE disc \
+--dataset=/home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/raw.loom \
+--out-dir=/home/yuanhao/DISC_imputation_result/RETINA_1.1.1_4 \
+--min-expressed-cell=49 \
+--library-size-factor=median
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_4/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+30 1.4 "" "retina"
+
+R --slave < "/home/yuanhao/github_repositories/DISC/reproducibility/Down-stream Analysis Improvement/raw_scripts/cluster_fn_0.3.r" \
+--args /home/yuanhao/DISC_imputation_result/RETINA_1.1.1_4/result/imputation.loom \
+"" /home/yuanhao/github_repositories/DISC/reproducibility/data/RETINA/cell_type.rds \
+50 1.4 "" "retina"
+