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.gitignore
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# Byte-compiled / optimized / DLL files
__pycache__/
# Jupyter Notebook
.ipynb_checkpoints
# python cache
.pyc
# data are too large to store on github local copies are stored in data folder
/data/*.parquet
# R files
.RData
.Rhistory
# results
1.Exploratory_Data_Analysis/results/*
2.Nomic_nELISA_Analysis/0.Exploratory_Analysis/PBMC/results/*
2.Nomic_nELISA_Analysis/0.Exploratory_Analysis/PBMC/results/*.log
2.Nomic_nELISA_Analysis/0.Exploratory_Analysis/SHSY5Y/results/*
2.Nomic_nELISA_Analysis/0.Exploratory_Analysis/SHSY5Y/results/*.log
# all csvs in 6.bulk_Morphology_Elastic_Network
6.bulk_Morphology_Elastic_Network/**/*.csv
11.bulk_Morphology_Elastic_Network_LOCO/**/*.csv
# do not add .tsv indexes
5.sc_Morphology_Logistic_Regression/0.split_data/indexes/*
5.sc_Morphology_Logistic_Regression/2.test_model/results/single_class/*
# vscode
.vscode/
# model results
4.sc_Morphology_Neural_Network_MLP_Model/results/*
# model indexes
4.sc_Morphology_Neural_Network_MLP_Model/0.hyperparameter_optimization/indexes/*
# index files
4.sc_Morphology_Neural_Network_MLP_Model/0.hyperparameter_optimization/indexes/*
6.bulk_Morphology_Elastic_Network/0.split_data/indexes/*
# results
6.bulk_Morphology_Elastic_Network/1.train_models/models/*
# model indexes
4.sc_Morphology_Neural_Network_MLP_Model/0.hyperparameter_optimization/indexes/*
# model results
7.redundancy_analysis/results/*
# Rplots intermediate files
*Rplots.pdf
8.cytopick_analysis/figures/*
8.cytopick_analysis/results/*
# images
figures/3.figure3/figures/images/*
figures/3.figure3/figures/composite_images/*
# results
figures/3.figure3/results/*
# mAP
9.mAP/data/*
# logs
9.mAP/notebooks/*.log
9.mAP/scripts/*.log
1.Exploratory_Data_Analysis/output/
# running scripts for model training
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/job_ids.txt
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/list_completed_jobs.txt
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/list_failed_jobs.txt
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/list_other_jobs.txt
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/list_timeout_jobs.txt
11.bulk_Morphology_Elastic_Network_LOCO/1.train_models/.nfs*
11.bulk_Morphology_Elastic_Network_LOCO/2.test_models/results/*
12.LOCO_BULK_MLP/figures/*
12.LOCO_BULK_MLP/results/*
12.LOCO_BULK_MLP/trained_models/*