Cross-species: linear models analysis of genes and genesets associations with MLS and other species traits.

To reproduce the linear analysis:

1. Get the genes and genesets datasets data from the link below. There can be found 2 folders for generating the genes XSPECIES_GENES and genesets XSPECIES_GENESETS_KEGG datasets, respectively. https://drive.google.com/drive/folders/16UI0VxdwCNrHZ1gRmhpZBJK1t-oJk2Ji?usp=sharing

2. Install and activate the environment necessary for running the code.

conda env create -f environment.yml
conda activate xspecies

3. Run the analysis via a CLI interface. From the repository's directory:

# Generate results for genes
python linearmodels.py --type_input genes analyze-models PATH_TO_GENES_DATASET_DIR OUTPUT_PATH_FOR_GENES_MODELS_DIR
python linearmodels.py --type_input genes extract-results OUTPUT_PATH_FOR_GENES_MODELS_DIR OUTPUT_PATH_GENES_SUMMARY_DIR

# Generate results for genesets
python linearmodels.py --type_input genesets analyze-models PATH_TO_GENESETS_DATASET_DIR OUTPUT_PATH_FOR_GENESETS_MODELS_DIR
python linearmodels.py --type_input genesets extract-results OUTPUT_PATH_FOR_GENESETS_MODELS_DIR OUTPUT_PATH_GENESETS_SUMMARY_DIR

# CLI interface help:
python linearmodels.py --help

4. Explore the results in OUTPUT_PATH_GENES_SUMMARY_DIR and OUTPUT_PATH_GENESETS_SUMMARY_DIR.