Here some useful scripts for biological networks analysis are available.
#Script for enrichment neighbourhood analysis: This Script is using module Graph available in CPAN developed by Jarkko Hietaniem
http://search.cpan.org/dist/Graph/lib/Graph.pod
For the GO enrichment analysis this script is using Go:TermFinder Perl module available in CPAN developed for Gavin Sherlock, Elizabeth Boyle and Ihab Awad.
http://search.cpan.org/dist/GO-TermFinder/lib/GO/TermFinder.pm
The idea is obtain for a nodes input list its neighbours and then analyze enrichment GO term in these lists.
You need download an association file http://www.geneontology.org/GO.downloads.annotations.shtml from Gene Ontology web site corresponding to your model organism and a Gene Ontology.obo file from http://www.geneontology.org/GO.downloads.ontology.shtml (OBO format)
#The script let the random remotion of links without replacement. So you have to provide the amount of rows (edges) to remove and the input network to process(pairwise format).
#The script let prepare networks for Alluvial comparion by Mapping Change Mapping change Rosvall & Bergstrom, Plos One (2010). Holmgren, Edler, and Rosvall�Appl. Netw. Sci. 8, 42 (2023)