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README_CONFIGURATION.rst

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DEFAULT

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

PATHS

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.

EXP_FILE

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