{"id":274,"date":"2016-09-17T00:35:16","date_gmt":"2016-09-16T22:35:16","guid":{"rendered":"http:\/\/almaaslab.nt.ntnu.no\/labsite\/?page_id=274"},"modified":"2022-05-12T09:17:49","modified_gmt":"2022-05-12T07:17:49","slug":"complex-network-analysis","status":"publish","type":"page","link":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/resources\/complex-network-analysis\/","title":{"rendered":"Complex Network Analysis"},"content":{"rendered":"<h5>Many of the software codes available for download are intended to be executed\u00a0from command line shell.<\/h5>\n<ul>\n<li>\n<h5><strong>S-core network peeling algorithms:<\/strong><\/h5>\n<ul>\n<li>Publication: M. Eidsaa and E. Almaas. Phys. Rev. E. 88, 062819 (2013). <span style=\"color: #ff0000;\"><a style=\"color: #ff0000;\" href=\"http:\/\/journals.aps.org\/pre\/abstract\/10.1103\/PhysRevE.88.062819\">[Link]<\/a><\/span><\/li>\n<\/ul>\n<ul>\n<li>Publication: M. Eidsaa, L. Stubbs and E. Almaas.<span style=\"color: #000000;\">\u00a0PLoS ONE 12, e0187611 (2017).\u00a0[<\/span><a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0187611\" target=\"_blank\" rel=\"noopener noreferrer\">Link<\/a><span style=\"color: #000000;\">]<\/span><\/li>\n<li>Network data sets and s-core+ algorithm:\n<ul>\n<li>README file, describing network and code (3kB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/s-core_plus\/README.txt\">README.txt<\/a>]<\/li>\n<li>The four gene co-expression wTO networks (723 MB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/s-core_plus\/networks.tgz\">networks.tgz<\/a>]<\/li>\n<li>Perl script for s-core+ method (5kB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/s-core_plus\/s-core_plus.pl\">s-core_plus.pl<\/a>]<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li>\n<h5><strong>Differential co-expression network analyses:<\/strong><\/h5>\n<ul>\n<li>Publication: A. Voigt, K. Nowick, and E. Almaas. PLoS Comput Biol (2017).<\/li>\n<li>Network data sets:\n<ul>\n<li>List of genes present in the CSD network (12 kB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/CSD_gene_list.txt\">CSD_gene_list.txt<\/a>]<\/li>\n<li>Complete list of genes with gene-expression data (117 kB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/complete_gene_list.txt\">complete_gene_list.txt<\/a>]<\/li>\n<li>Link-list for CSD network (68 kB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/CSD_network.txt\">CSD_network.txt<\/a>]<\/li>\n<li>Complete list\u00a0of correlations, variance\u00a0of the correlations, and CSD-scores (11 GB): [<a href=\"http:\/\/almaaslab.nt.ntnu.no\/downloads\/CSD_complete_data.txt.gz\">CSD_complete_data.txt.gz<\/a>]<\/li>\n<li>Software programs used in the analysis in this paper is available on GitHub: [<a href=\"https:\/\/github.com\/andre-voigt\/CSD\">CSD_git<\/a>]<\/li>\n<\/ul>\n<\/li>\n<li>A general purpose R-code for CSD-calculations available on GitHub: [<a href=\"https:\/\/github.com\/AlmaasLab\/csdR\" target=\"_blank\" rel=\"noopener\">CSD_R<\/a>]<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<ul>\n<li><strong>Microbial co-occurrence analysis:<\/strong>\n<ul>\n<li>A general purpose R-code for analyzing OTU tables and generate (1) co-occurrence tables or (2) Lotka-Volterra time-dynamics of the system: [<a href=\"https:\/\/github.com\/AlmaasLab\/micInt\" target=\"_blank\" rel=\"noopener\">micInt<\/a>]<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Many of the software codes available for download are intended to be executed\u00a0from 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.\u00a0PLoS ONE 12, e0187611 (2017).\u00a0[Link] Network data sets and s-core+ algorithm: README file, describing network [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":252,"parent":2,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-274","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/pages\/274","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/comments?post=274"}],"version-history":[{"count":19,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/pages\/274\/revisions"}],"predecessor-version":[{"id":10302,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/pages\/274\/revisions\/10302"}],"up":[{"embeddable":true,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/pages\/2"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/media\/252"}],"wp:attachment":[{"href":"https:\/\/almaaslab.nt.ntnu.no\/index.php\/wp-json\/wp\/v2\/media?parent=274"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}