{"id":31,"date":"2019-11-18T05:24:42","date_gmt":"2019-11-18T05:24:42","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/binzhanglab\/?page_id=31"},"modified":"2019-11-19T15:58:20","modified_gmt":"2019-11-19T15:58:20","slug":"resources","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"<p><em><span style=\"text-decoration: underline\"><strong>Software tools<\/strong><\/span><\/em><\/p>\n<p><strong>Multiscale Network Analysis<\/strong><\/p>\n<ul>\n<li>Link to presentation: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pdfs\/BinZhang_Lecture1_Mutiscale-Networks.pdf\">PDF<\/a><\/li>\n<\/ul>\n<p><strong>\u00a0Multiscale Network Modeling in Alzheimer&#8217;s Disease<\/strong><\/p>\n<ul>\n<li>Link to presentation: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pdfs\/BinZhang_Lecture3_AD-Networks.pdf\">PDF<\/a><\/li>\n<\/ul>\n<p><strong>\u00a0Key Driver Analysis<\/strong><\/p>\n<ul>\n<li>Link to presentation: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pdfs\/BinZhang_Lecture2_KeyDriverAnalysis.pdf\">PDF<\/a><\/li>\n<li>Link to demo presentation: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pdfs\/BinZhang_Lecture4_Demo.pdf\">PDF<\/a><\/li>\n<li>Link to paper: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pdfs\/KDA_WCE2013.pdf\">PDF<\/a><\/li>\n<li>Link to R package: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pkgs\/KDA_0.2.2.zip\">ZIP<\/a>(windows), <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/pkgs\/KDA_0.2.2.tar.gz\">GZ<\/a>(Linux)<\/li>\n<\/ul>\n<p><strong>\u00a0MEGENA: Multiscale Embeded Gene coExpression Network Analysis<\/strong><\/p>\n<ul>\n<li>Link to the paper: <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1004574\">DOI<\/a>, <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/publications\/MEGENA_journal.pcbi.1004574.pdf\">PDF<\/a><\/li>\n<li>Link to tutorial: <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/publications\/MEGENA_tutorial.pdf\">PDF<\/a><\/li>\n<li>Link to R package: <a href=\"https:\/\/github.com\/songw01\/MEGENA\/\">github<\/a> &amp; <a href=\"https:\/\/cran.r-project.org\/web\/packages\/MEGENA\/index.html\">CRAN<\/a><\/li>\n<\/ul>\n<p><strong>\u00a0SuperExactTest: Efficient Test and Visualization of Multi-Set Intersections<\/strong><\/p>\n<ul>\n<li>Link to the paper: <a href=\"https:\/\/doi.org\/10.1038\/srep16923\">DOI<\/a>, <a href=\"https:\/\/github.com\/mw201608\/mnml-public\/blob\/master\/publications\/SuperExactTest_srep16923.pdf\">PDF<\/a><\/li>\n<li>Link to the tutorial: <a href=\"https:\/\/cran.r-project.org\/web\/packages\/SuperExactTest\/vignettes\/set_html.html\">LINK<\/a><\/li>\n<li>Link to R package: <a href=\"https:\/\/github.com\/mw201608\/SuperExactTest\/\">github<\/a> &amp; <a href=\"https:\/\/cran.r-project.org\/web\/packages\/SuperExactTest\/index.html\">CRAN<\/a><\/li>\n<\/ul>\n<p><strong>NetWeaver: Graphic Presentation of Complex Genomic and Network Data Analysis<br \/>\n<\/strong><\/p>\n<ul>\n<li>Link to the paper: <a href=\"https:\/\/doi.org\/10.1186\/s13073-016-0355-3\">DOI<\/a><\/li>\n<li>Link to the tutorial: <a href=\"https:\/\/github.com\/mw201608\/NetWeaver\/blob\/master\/examples\/netweaver.Md\">LINK<\/a><\/li>\n<li>Link to R package: <a href=\"https:\/\/github.com\/mw201608\/NetWeaver\">github<\/a> &amp; <a href=\"https:\/\/cran.rstudio.com\/web\/packages\/NetWeaver\/index.html\">CRAN<\/a><\/li>\n<\/ul>\n<p><strong>sunburst.shiny: R\/Shiny App for Interactive Visualization of Sunburst Network Hierarchy<br \/>\n<\/strong><\/p>\n<ul>\n<li>Link to the shiny app: <a href=\"https:\/\/github.com\/mw201608\/sunburst.shiny\">github<\/a> &amp; <a href=\"https:\/\/network.shinyapps.io\/sunburst\/\">shinyapps.io<\/a><\/li>\n<\/ul>\n<p class=\"c-article-title u-h1\"><span style=\"text-decoration: underline\"><strong><em>Datasets<\/em><\/strong><\/span><\/p>\n<p class=\"c-article-title u-h1\"><strong>Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer&#8217;s disease<\/strong><\/p>\n<ul>\n<li>Link to the paper: DOI:<a href=\"https:\/\/doi.org\/10.1038\/sdata.2018.185\">10.1038\/sdata.2018.185<\/a><\/li>\n<li>The Mount Sinai Brain Bank (MSBB) study description (DOI<a title=\"\" href=\"https:\/\/doi.org\/10.7303\/syn3159438\">:10.7303\/syn3159438<\/a>)<\/li>\n<li>Metadata (DOI:<a href=\"https:\/\/doi.org\/10.7303\/syn7392158\">10.7303\/syn7392158<\/a>)<\/li>\n<li>RNA-seq gene expression (DOI:<a href=\"https:\/\/doi.org\/10.7303\/syn3157743\">10.7303\/syn3157743<\/a>)<\/li>\n<li>Whole Exome Sequencing (DOI:<a href=\"https:\/\/doi.org\/10.7303\/syn4645334\">10.7303\/syn4645334<\/a>)<\/li>\n<li>Whole Genome Sequencing (DOI:<a href=\"https:\/\/doi.org\/10.7303\/syn10901600\">10.7303\/syn10901600<\/a>)<\/li>\n<li>Proteomics (Label Free Mass Spectrometry) (DOI:<a href=\"https:\/\/doi.org\/10.7303\/syn5759470\">10.7303\/syn5759470<\/a>)<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Software tools Multiscale Network Analysis Link to presentation: PDF \u00a0Multiscale Network Modeling in Alzheimer&#8217;s Disease Link to presentation: PDF \u00a0Key Driver Analysis Link to presentation: PDF Link to demo presentation: PDF Link to paper: PDF Link to R package: ZIP(windows), GZ(Linux) \u00a0MEGENA: Multiscale Embeded Gene coExpression Network Analysis Link to the paper: DOI, PDF Link [&hellip;]<\/p>\n","protected":false},"author":387,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-31","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/pages\/31","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/users\/387"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/comments?post=31"}],"version-history":[{"count":10,"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/pages\/31\/revisions"}],"predecessor-version":[{"id":107,"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/pages\/31\/revisions\/107"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/binzhanglab\/wp-json\/wp\/v2\/media?parent=31"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}