If you want to use HOODS to perform large-scale analyses, we recommend that you download the command-line version of the program and run it locally on your own computer. HOODS is implemented in Perl and relies on no modules or external programs.
To run HOODS, execute the following command:
./hoods.pl <matrix file> <label file> [alpha]
The first argument is the name of file containing a similarity matrix; this file has three columns, namely entity1, entity2, and similarity. The second argument is the name of a label file with two columns, namely entity and association score. The third optional argument is the value for alpha, which defaults to 0.5.
The script produces a tab-separated file with all the neighborhoods ranked by their neighborhood score. Each line in the file lists the score of a neighborhood, the number of entities in the neighborhood, and a list of all of them.
Released under the 3-clause BSD license.