processing_data

.gitignore

@@ -171,11 +171,11 @@ Wave1_data/3.cellprofiling/analysis_output/*
 Wave1_data/4.processing_profiled_features/notebooks/runinfo/*
 Wave1_data/4.processing_profiled_features/scripts/runinfo/*
 Wave1_data/4.processing_profiled_features/data/*
-
-Wave1_data/5.exploratory_data_analysis/data/*
-Wave1_data/5.exploratory_data_analysis/figures/*
-
 # slurm logs
 *.out
 *.err
 *.log
+Wave1_data/5.exploratory_data_analysis/scripts/Rplots.pdf
+Wave1_data/5.exploratory_data_analysis/data/*
+Wave1_data/5.exploratory_data_analysis/figures/*
+

Wave1_data/4.processing_profiled_features/0.merge_sc.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=32
+#SBATCH --partition=amilan
+#SBATCH --mem=100G
+#SBATCH --qos=normal
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=merge_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+python 0.merge_sc.py
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Merge sc processing completed."

Wave1_data/4.processing_profiled_features/1.annotate_sc.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=2
+#SBATCH --partition=amilan
+#SBATCH --mem=100G
+#SBATCH --qos=normal
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=annotate_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+python 1.annotate_sc.py
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Annotate sc processing completed."

Wave1_data/4.processing_profiled_features/2.combine_sc.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --partition=amem
+#SBATCH --mem=300G
+#SBATCH --qos=mem
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=combine_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+python 2.combine_sc.py
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Combing sc processing completed."

Wave1_data/4.processing_profiled_features/3.normalize_sc.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --ntasks=16
+#SBATCH --partition=amem
+#SBATCH --mem=300G
+#SBATCH --qos=mem
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=normalize_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+
+python 3.normalize_sc_across_time.py
+python 3.normalize_sc_within_time.py
+python 3.normalize_sc_against_first_time.py
+
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Normalizing sc processing completed."

Wave1_data/4.processing_profiled_features/4.feature_select_sc.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --partition=amem
+#SBATCH --mem=750G
+#SBATCH --qos=mem
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=fs_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+python 4.feature_select_sc.py
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Feature_selection processing completed."

Wave1_data/4.processing_profiled_features/5.aggregate_sc.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+#SBATCH --nodes=1
+#SBATCH --partition=amem
+#SBATCH --mem=300G
+#SBATCH --qos=mem
+#SBATCH --account=amc-general
+#SBATCH --time=24:00:00
+#SBATCH --output=fs_sc-%j.out
+
+# activate  cellprofiler environment
+module load anaconda
+conda init bash
+conda activate cellprofiler_timelapse_env
+
+jupyter nbconvert --to=script --FilesWriter.build_directory=scripts/ notebooks/*.ipynb
+
+cd scripts/ || exit
+
+python 5.aggregate_profiles.py
+
+cd ../ || exit
+
+# deactivate cellprofiler environment
+conda deactivate
+
+echo "Aggregation completed."