scripts

Scripts

build_synnet.sh

This script creates a SynNet taking as inputs FASTA and BED files.

Print usage:

./build_synnet.sh

Print help:

./build_synnet.sh -h

extract_subnetwork.sh

This scripts extracts a subnetwork from a SynNet with a list of ids in a text file.

Print usage:

./extract_subnetwork.sh

get_node_table.sh and get_node_table_clusters.sh

These scripts have the same functionality, they create a metadata table for nodes taking as inputs a SynNet (get_node_table.sh) or community (get_node_table_clusters.sh) file and a metadata table. The only difference is the fields where the scripts look for the network edges (columns 3 and 4 for get_node_table.sh, and columns 1 and 2 for get_node_table.clusters.sh).

Print usage:

./get_node_table.sh
./get_node_table_clusters.sh

phylogenetic_profiling.R

R script used to create a phylogenetic profiling figure. Instructions about how to use it come in the book chapter.