{"id":1334,"date":"2018-01-19T08:33:17","date_gmt":"2018-01-19T13:33:17","guid":{"rendered":"http:\/\/my.vanderbilt.edu\/irishlab\/?p=1334"},"modified":"2018-01-19T08:54:28","modified_gmt":"2018-01-19T13:54:28","slug":"published-2018-diggins-et-al-current-protocols-in-cytometry","status":"publish","type":"post","link":"https:\/\/my.vanderbilt.edu\/irishlab\/2018\/01\/published-2018-diggins-et-al-current-protocols-in-cytometry\/","title":{"rendered":"Published: 2018 Diggins et al., Current Protocols in Cytometry"},"content":{"rendered":"<p style=\"text-align: justify\">Congrats to Kirsten Diggins, Jocelyn Gandelman, and Caroline Roe on their publication!\u00a0 This protocol aggregates code, scripts, and examples for MEM that we use regularly in courses and research:<\/p>\n<p style=\"text-align: justify\">Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell Identity Labels with Marker Enrichment Modeling (MEM).\u00a0<strong><em>Current Protocols in Cytometry<\/em>\u00a0<\/strong>2017. NIHMS912131. PMC in progress. \u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/29345329\">Pubmed<\/a>. \u00a0<a href=\"https:\/\/doi.org\/10.1002\/cpcy.34\">DOI<\/a>.<\/p>\n<p style=\"text-align: justify\">\u25ba This peer-reviewed protocol is targeted for a biology background audience and describes in detail the steps needed to obtain and run code for Marker Enrichment Modeling (MEM) in R\/flowCore using text, CSV, or flow cytometry standard (FCS) files.\u00a0 MEM was <a href=\"http:\/\/my.vanderbilt.edu\/irishlab\/2017\/03\/diggins-et-al-nature-methods-2017\/\">originally described<\/a> in Diggins et al., <em>Nature Methods<\/em> 2017 (<a href=\"https:\/\/doi.org\/10.1038\/nmeth.4149\">DOI<\/a>).\u00a0 Since publication, MEM has been successfully applied to identify subgroups in a wide variety of data types, including fluorescence cytometry, mass cytometry, single cell RNA-seq, quantitative imaging, gene expression profiling, and clinical phenotyping of patients.<\/p>\n<div id=\"attachment_1338\" style=\"width: 2323px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-1338\" class=\"size-full wp-image-1338\" src=\"https:\/\/cdn.vanderbilt.edu\/t2-my\/my-prd\/wp-content\/uploads\/sites\/424\/2018\/01\/2018-Figure-10.jpg\" alt=\"Diggins et al., Current Protocols in Cytometry - Measure and share cell identity with a MEM label\" width=\"2313\" height=\"1171\" \/><p id=\"caption-attachment-1338\" class=\"wp-caption-text\">Diggins et al., Current Protocols in Cytometry &#8211; Measure and share cell identity with a MEM label<\/p><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Congrats to Kirsten Diggins, Jocelyn Gandelman, and Caroline Roe on their publication!\u00a0 This protocol aggregates code, scripts, and examples for MEM that we use regularly in courses and research: Diggins KE, Gandelman JS, Roe CE, Irish JM. Generating Quantitative Cell &hellip; <a href=\"https:\/\/my.vanderbilt.edu\/irishlab\/2018\/01\/published-2018-diggins-et-al-current-protocols-in-cytometry\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":565,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[1],"tags":[],"class_list":["post-1334","post","type-post","status-publish","format-standard","hentry","category-news"],"_links":{"self":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/1334","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/users\/565"}],"replies":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/comments?post=1334"}],"version-history":[{"count":5,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/1334\/revisions"}],"predecessor-version":[{"id":1347,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/posts\/1334\/revisions\/1347"}],"wp:attachment":[{"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/media?parent=1334"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/categories?post=1334"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/irishlab\/wp-json\/wp\/v2\/tags?post=1334"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}