minimum_log2_fold_change: Minimum value of log2 fold change for determining up-regulated genes
maximum_log2_fold_change: Maximum value of log2 fold change for determining down-regulated genes
maximum_adjusted_p_value: Maximum value of adjusted p-value, used as additional criteria for determining differentially expressed genes
input_directory: Home directory for input files. If you prefer not to have such a directory, leave empty and then give absolute paths for input files
output_directory: Home directory for output files
protein_protein_interaction_graph: Path to protein-protein interaction graph w.r.t. input_directory. Details can be found in README.md
experiment_file: Path to experiment file w.r.t. input_directory. Details can be found in README.md
drug_targets_file: Path to drug targets file w.r.t. input_directory. Details can be found in README.md
transcription_factors_file: Path to transcription factors file w.r.t. input_directory. Details can be found in README.md. This file is not mandatory, leave blank after = sign, if you prefer not to give this information.
base_mean_name: Column name for base mean
log2_fold_change_name: Column name for log2 fold change
adjusted_p_value_name: Column name for adjusted p value
entrez_id_name: Column name for Entrez id
split_character: If there are multiple Entrez ids and symbols in a cell, the character that separates them
sheet_name: The name of the sheet. Can be left empty if the experiment_file is a csv file