Many of the software codes available for download are intended to be executed from command line shell.

• S-core network peeling algorithms:

  • Publication: M. Eidsaa and E. Almaas. Phys. Rev. E. 88, 062819 (2013). [Link]
  • Publication: M. Eidsaa, L. Stubbs and E. Almaas. PLoS ONE 12, e0187611 (2017). [Link]
  • Network data sets and s-core+ algorithm:
    • README file, describing network and code (3kB): [README.txt]
    • The four gene co-expression wTO networks (723 MB): [networks.tgz]
    • Perl script for s-core+ method (5kB): [s-core_plus.pl]

• Differential co-expression network analyses:

  • Publication: A. Voigt, K. Nowick, and E. Almaas. PLoS Comput Biol (2017).
  • Network data sets:
    • List of genes present in the CSD network (12 kB): [CSD_gene_list.txt]
    • Complete list of genes with gene-expression data (117 kB): [complete_gene_list.txt]
    • Link-list for CSD network (68 kB): [CSD_network.txt]
    • Complete list of correlations, variance of the correlations, and CSD-scores (11 GB): [CSD_complete_data.txt.gz]
    • Software programs used in the analysis in this paper is available on GitHub: [CSD_git]
  • A general purpose R-code for CSD-calculations available on GitHub: [CSD_R]

 

• Microbial co-occurrence analysis:
  • A general purpose R-code for analyzing OTU tables and generate (1) co-occurrence tables or (2) Lotka-Volterra time-dynamics of the system: [micInt]