{"id":405,"date":"2015-10-20T09:57:01","date_gmt":"2015-10-20T14:57:01","guid":{"rendered":"https:\/\/my.vanderbilt.edu\/irishlab\/?page_id=405"},"modified":"2015-10-20T09:57:01","modified_gmt":"2015-10-20T14:57:01","slug":"cytometry-analysis-visne-spade-heatmaps","status":"publish","type":"page","link":"https:\/\/www.irishlab.org\/index.php\/protocols\/cytometry-analysis-visne-spade-heatmaps\/","title":{"rendered":"Cytometry analysis: viSNE, SPADE, &#038; Heatmaps"},"content":{"rendered":"<p><a href=\"http:\/\/localhost\/irishv01\/wp-content\/uploads\/2015\/10\/Slide1.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"alignleft size-medium wp-image-409\" src=\"https:\/\/my.vanderbilt.edu\/irishlab\/files\/2015\/10\/Slide1-300x225.jpg\" alt=\"\" width=\"300\" height=\"225\" srcset=\"https:\/\/www.irishlab.org\/wp-content\/uploads\/2015\/10\/Slide1-300x225.jpg 300w, https:\/\/www.irishlab.org\/wp-content\/uploads\/2015\/10\/Slide1-768x576.jpg 768w, https:\/\/www.irishlab.org\/wp-content\/uploads\/2015\/10\/Slide1.jpg 960w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a>These slides are from an advanced cytometry data analysis course based on the methods recently published (<a title=\"Diggins et al. Methods 2015 - Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data\" href=\"http:\/\/dx.doi.org\/10.1016\/j.ymeth.2015.05.008\">Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data<\/a>. Diggins KE, Ferrell PB, Irish JM,\u00a0<em>Methods.<\/em> 2015.). \u00a0Please cite this manuscript when referencing this course or methods from it, such as sequential analysis with multiple tools and related modular, unsupervised workflows.<\/p>\n<p><span style=\"font-size: 13px\">This course was taught at the 2015 Australasian Cytometry Society (ACS) meeting in a master class by Jonathan Irish. \u00a0The slides and course content were developed by Jonathan Irish, Kirsten Diggins, &amp; Brent Ferrell. \u00a0All materials, images, and slides are copyright (c) 2015 by Jonathan Irish, All Rights Reserved. <\/span><\/p>\n<p><span style=\"font-size: 13px\">This course uses a free trial of Cytobank and publicly available data to go through data analysis with viSNE, SPADE, and heatmaps in Cytobank and R. \u00a0All of the starting and intermediate files are available online as well as instructions and slides providing context.<\/span><\/p>\n<h3>Cytometry analysis with viSNE, SPADE, and heatmaps<\/h3>\n<p>A PDF of the images below is available here:<\/p>\n<p><a href=\"http:\/\/localhost\/irishv01\/wp-content\/uploads\/2015\/10\/2015-10-Methods-Course-Diggins-Perth-Advanced-Clustering-Approaches-v3-shown-deanimated-v2.pdf\">2015-10 Methods Course Diggins Perth &#8211; Advanced Clustering Approaches v3 &#8211; shown &#8211; deanimated v2<\/a><\/p>\n<p>All the FCS files are available on Cytobank. \u00a0You can sign up for a free 1 month trial to get access to viSNE, SPADE, and more here:<\/p>\n<p><a title=\"Sign up for Cytobank, 1 month free access to viSNE, SPADE, and more\" href=\"https:\/\/premium.cytobank.org\/cytobank\/signup\/\">https:\/\/premium.cytobank.org\/cytobank\/signup\/<\/a><\/p>\n<p>(Note Cytobank is commercial software developed by Dr. Irish and others at Cytobank Inc.)<\/p>\n<p><span style=\"font-size: 13px\">An experiment containing all the course materials is here on the Premium Cytobank server:<\/span><\/p>\n<p><a title=\"Diggins et al. Methods 2015 Data analysis course files\" href=\"https:\/\/premium.cytobank.org\/cytobank\/experiments\/44410\/\">https:\/\/premium.cytobank.org\/cytobank\/experiments\/44410\/<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>These slides are from an advanced cytometry data analysis course based on the methods recently published (Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data. Diggins KE, Ferrell PB, Irish JM,\u00a0Methods. 2015.). \u00a0Please cite this manuscript when referencing this course or methods from it, such as sequential analysis with multiple [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":71,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-405","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/pages\/405","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/comments?post=405"}],"version-history":[{"count":0,"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/pages\/405\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/pages\/71"}],"wp:attachment":[{"href":"https:\/\/www.irishlab.org\/index.php\/wp-json\/wp\/v2\/media?parent=405"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}