Commit 31b0918f authored by Nicasia Beebe-Wang's avatar Nicasia Beebe-Wang
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Update README.md

parent f12f63fd
......@@ -13,7 +13,7 @@ Although biological pathways are essential for interpreting results from computa
### Resources
**Community_Members.xlsx** and **Community_Members.csv** files contain the list of all pathways included in each of the 35 pathway communities we learned.
**Community_kmers.xlsx** and **Community_kmers.csv** files contain the list of k-mers for each pathway community, along with the number of occurence and hubness of each pathway.
**Community_kmers.xlsx** and **Community_kmers.csv** files contain the list of k-mers for each pathway community, along with the number of occurence and hubness of each pathway (within the community's subgraph).
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......@@ -30,13 +30,15 @@ Although biological pathways are essential for interpreting results from computa
#### 2. Comparison of clustering algorithms
**algorithm_helpers.py** is the helper script to run various clustering and community detection algorithms.
**CNM_networkx.py** is the modified version of the CNM algorithm.
**CNM_networkx.py** is a modified version of the CNM algorithm (which allows us to select the number of communities to generate) originally from [NetworkX]( https://networkx.github.io/documentation/stable/_modules/networkx/algorithms/community/modularity_max.html).
**select_resolution_for_Louvain.ipynb** script selects the best resolution for the Louvain algorithm for each database category.
**comparison_of_algorithms.ipynb** script executes all the clustering algorithms and compares them across all pathway databases.
#### 3. Generating combined pathway network and learning communities
**combined_graph_louvain_with_weights.ipynb** defines the combined pathay network and applies Louvain algoritm to learn pathway communities.
**Full_graph_louvain_with_weights_community_labels** includes the community labels learned by different resolutions.
**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_community_sizes_and_distributions.ipynb** investigates the size and pathway distribution for each pathway community.
**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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