GitHub - kthuang20/LINCS_repurposing: Predicting New Indications for Known Drugs Based on Similarity in Drug Signatures

This project uses the following resources:

This GitHub repository contains the following jupyter notebooks:

1. Generating DRH datasets.ipynb -- This notebook describes the steps taken to prepare the Drug Repurposing Hub (DRH) datasets later used to train the model.
2. Generating Connectivity Scores.ipynb -- This notebook describes the steps taken to generate the file containing all the connectivity scores used to compare to our proposed model based on spearman correlation.
3. Preliminary Analysis (Fig 1).ipynb -- This notebook compares the performance of a model based on connectivity scores vs. our proposed model and generates Figures 1a and 1b.
4. Exploring Impact of TAS (Fig 2).ipynb -- This notebook describes the steps taken to compare how the TAS might affect the performance of our proposed model, generating Figures 2a and 2b.
5. Generating the Clinical Trials Datasets.ipynb -- This notebook details the steps taken to generate the clinical trials datasets, later used to evaluate how well our model can predict for new uses of drugs.
6. Evaluate Model (Figure 3).ipynb -- This notebook details the steps taken to generate the weighted average ensemble model combining predictions across all cell lines and evaluating its performance for new experimental uses. This notebook generates Figures 3a and 3b.

Other relevant information:

The conn_scores folder contains the files used to generate the conn_scores.txt file used to generate Figure 1b.
The DRH_clin_data folder contains the DRH datasets datasets used to train and evaluate the model
The ref_data folder contains the files relevant to the LINCS L1000 data and files used to prepare the DRH and clinical trial datasets.
The environment.yml file specifies the dependencies of the conda environment used for all analyses performed.
The model_predictions.txt file contains the ensemble model's predictions for drug indications in clinical trials data.

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Name		Name	Last commit message	Last commit date
Latest commit History 18 Commits
DRH_clin_data		DRH_clin_data
conn_scores		conn_scores
ref_data		ref_data
.gitignore		.gitignore
1. Generating DRH datasets.ipynb		1. Generating DRH datasets.ipynb
2. Generating Connectivity Scores.ipynb		2. Generating Connectivity Scores.ipynb
3. Preliminary Analysis (Fig 1).ipynb		3. Preliminary Analysis (Fig 1).ipynb
4. Exploring Impact of TAS (Fig 2).ipynb		4. Exploring Impact of TAS (Fig 2).ipynb
5. Generating the Clinical Trials Datasets.ipynb		5. Generating the Clinical Trials Datasets.ipynb
6. Evaluate Model (Figure 3).ipynb		6. Evaluate Model (Figure 3).ipynb
README.md		README.md
environment.yml		environment.yml
model_predictions.txt		model_predictions.txt