R and Python code for Science Translational Medicine Manuscript abl5849

R Code

Rand_Alloc_Peak_Templates.r, script for performing random allocation of subjects to Discovery or Replication sets.

Regression_Models_Main.r, script for fitting Elastic net, LASSO and Ridge models on main GcGc matrix. Script also performs batch effect adjustment.

Regression_Models_Air_Supply_Room_Air.r, script for fitting Elastic net, LASSO and Ridge models on GcGc matrix for air supply and room air.

Graphs_by_Group.r, script for generating graphs for each disease group based on correlation matrix for 101 features. Script is also used to perform Louvain clustering on the graphs.

GSVA_models.r, script for generating graph for all disease groups (healthy excluded) ,discovery and replication combined. Graph based on correlation matrix for 101 features. Script is also used to perform Louvain clustering on the graph and feature enrichment.

Calculate_Scores.r, script for calculating example biomarker scores.

PYTHON Code

EMBER_TDA_Main.py, script for performing TDA using Kepler Mapper on GcGc matrix.