Commit 5bda07d1 authored by Ayse Berceste Dincer's avatar Ayse Berceste Dincer
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Update README.md

parent 8df2d385
......@@ -20,12 +20,10 @@ Although biological pathways are essential for interpreting results from computa
### Pipeline
- **pathways_raw** folder contains raw pathway files from MSigDB.
- **curated_hierarchies** folder contains the hierarchies and high-level categories for KEGG, REACTOME, and GO databases.
- **pipeline** folder contains all the scripts in our pipeline.
#### 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.
- **save_true_labels.ipynb** script records the true curated labels for each pathway category.
- **adj_matrices** and **curated_labels** folders contain the pathway adjacency matrices and curated labels for each pathway category, respectively.
#### 2. Comparison of clustering algorithms
......@@ -36,9 +34,8 @@ Although biological pathways are essential for interpreting results from computa
#### 3. Generating combined pathway network and learning communities
- **combined_graph_louvain_with_weights.ipynb** defines the combined pathay network and applies the Louvain algoritm to learn pathway communities.
- **Full_graph_louvain_with_weights_community_labels** includes the community labels learned using different resolutions.
#### 4. Analysis of combined pathway network
- **combined_graph_analyses/community_sizes_and_distributions.ipynb** investigates the size and pathway distribution for each pathway community.
- **combined_graph_analyses/curated_category_distributions_clustermaps.ipynb** generates cluster maps showing distributions of curated categories as they relate to our communities
- **combined_graph_analyses/generate_kmer_labels.ipynb** automatically generates labels for each community based on their members' names.
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- **combined_graph_analyses/generate_kmer_labels.ipynb** automatically generates labels for each community based on their members' names.
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