{"id":58,"date":"2024-03-24T21:41:04","date_gmt":"2024-03-24T21:41:04","guid":{"rendered":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/?page_id=58"},"modified":"2024-03-24T21:41:04","modified_gmt":"2024-03-24T21:41:04","slug":"software-developed-by-t-m-muralis-research-group","status":"publish","type":"page","link":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/software-developed-by-t-m-muralis-research-group\/","title":{"rendered":"SOFTWARE DEVELOPED BY T. M. MURALI&#8217;S RESEARCH GROUP"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">Please see our&nbsp;<a href=\"https:\/\/github.com\/Murali-group\/\">GitHub organisation<\/a>&nbsp;for active and recent software projects. This page lists older packages. We have released all software on this page under version 3 of the&nbsp;<a href=\"http:\/\/www.gnu.org\/copyleft\/gpl.html\">GNU General Public License<\/a>. Many of these individual packages are available as part of the&nbsp;<a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\">Biorithm software suite<\/a>. For packages that are part of Biorithm, the links below take you to the documentation for each package.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Network and Pathway Analysis\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/graphspace.org\/\">GraphSpace<\/a>, a website for uploading, sharing, and collaborating with networks.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software-downloads\/public\/dispatch.cgi\/software\/pathlinker\">PathLinker<\/a>,&nbsp;a path-based algorithm to reconstruct interactions in signaling pathways.<\/li>\n\n\n\n<li><a href=\"http:\/\/murali-group.github.io\/halp\/\">halp<\/a>, a library of algorithms for directed and undirected hypergraphs.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software-downloads\/public\/dispatch.cgi\/software\/xtalk\">XTalk<\/a>, a path-based approach for detecting crosstalk between signaling pathways.<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Data-Driven Systems Biology\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/downloads\/CRFE-1.0\/\">Concise, Functional Enrichment of Ranked Gene Lists<\/a>, a method to compute a small set of non-redundant functions that annotated a ranked list of genes.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/networklego.html\">NetworkLego<\/a>, find networks of molecular interactions activated in a cell state or in response to a particular perturbation or stimulus and compare and contrast these&nbsp;<em>active networks<\/em>&nbsp;to construct&nbsp;<em>network legos<\/em>, building blocks of the molecular interaction network.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/enrich.html\">Functional enrichment<\/a>, different methods for computing which sets of pre-defined genes (e.g., biological pathways) are over-represented in another set of genes, e.g., differentially-expressed genes in a treatment-control study.<\/li>\n\n\n\n<li><a href=\"http:\/\/bioinformatics.cs.vt.edu\/~cgrivera\/GraphHopper\">GraphHopper<\/a>, a method for finding conserved protein interaction networks.&nbsp;<em>This software is not part of Biorithm.<\/em><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Predicting Gene Function\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/gain.html\">GAIN<\/a>, a system for whole-genome prediction of gene functions<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Gene Expression Analysis\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/xmotif.html\">xMotif<\/a>, an algorithm for computing biclusters in gene expression data and (optionally) building nearest-neighbour sample classifiers based on these biclusters.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/bivoc.html\">BiVoC<\/a>, a system for automatic layout and visualisation of biclusters<\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>Data Mining\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/apriori.html\">Bicluster mining in binary matrices<\/a>, our implementation of a level-wise algorithm to find closed biclusters in binary matrices. This algorithm is similar to Apriori (it incrementally adds rows rather than columns), except that whenever it finds a new bicluster it immediately adds all possible rows that make the bicluster closed. The software outputs both the rows and columns of the biclusters it finds.<\/li>\n\n\n\n<li><a href=\"https:\/\/bioinformatics.cs.vt.edu\/~murali\/software\/biorithm\/truth-tables.html\">Truthiness mining<\/a>, a method to find truth tables in binary and categorical matrices.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Please see our&nbsp;GitHub organisation&nbsp;for active and recent software projects. This page lists older packages. We have released all software on this page under version 3 of the&nbsp;GNU General Public License. Many of these individual packages are available as part of the&nbsp;Biorithm software suite. For packages that are part of Biorithm, the links below take you [&hellip;]<\/p>\n","protected":false},"author":447,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-58","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/58","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/users\/447"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/comments?post=58"}],"version-history":[{"count":1,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/58\/revisions"}],"predecessor-version":[{"id":59,"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/pages\/58\/revisions\/59"}],"wp:attachment":[{"href":"https:\/\/wordpress.cs.vt.edu\/tmmurali\/wp-json\/wp\/v2\/media?parent=58"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}