@@ -24,6 +24,7 @@ Although knowledge of biological pathways is essential for interpreting results
#### 1. Generating adjacency matrices and curated hierarchies
-**gmts_to_adj_matrices.py** and **gmts_to_adj_matrices_offdiagonal.py** define adjacency matrices for the MSigDB pathways by measuring the pairwise similarities betweeen pathways from each database and across databases, respectively.
-**adj_matrices** and **curated_labels** folders contain the pathway adjacency matrices and curated labels for each pathway category, respectively.
-**pathway_overlaps.ipynb** is an analysis notebook which measures the overlaps among pathways for the visualization in Figure 1.
#### 2. Comparison of clustering algorithms
-**algorithm_helpers.py** is the helper script to run various clustering and community detection algorithms.
