{"id":13313,"date":"2013-03-11T18:14:18","date_gmt":"2013-03-11T18:14:18","guid":{"rendered":"http:\/\/\/sethduncan2.wpcomstaging.com\/d2\/advanced-features\/"},"modified":"2023-11-16T13:23:46","modified_gmt":"2023-11-16T21:23:46","slug":"advanced-features","status":"publish","type":"page","link":"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/","title":{"rendered":"Advanced Features"},"content":{"rendered":"<p class=\"lead\">FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data.<\/p>\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/\/sethduncan2.wpcomstaging.com\/advanced-features\/fj-acs\/\"><strong>Archival Cytometry Standard<\/strong><\/a> (ACS) are container files that compress workspaces, FCS data files, and plugin outputs into a single compressed .zip file, helpful for archiving, sharing, or working with remote data storage.<\/li>\n\n\n\n<li><strong><a href=\"http:\/\/\/sethduncan2.wpcomstaging.com\/advanced-features\/maketemplate\/\">Templates<\/a><\/strong> are an excellent way to expedite data analysis by applying a previous analysis to new data.&nbsp; &nbsp;A template contains the groups, gates, and statistics without the associated FCS files for re-use.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/embed-2\/\">Embed<\/a><\/strong>: Forward propagate clustering or dimensionality reduction results to new files with the same parameters.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/cluster-explorer\/\">Cluster Explorer<\/a><\/strong>: Display line charts, bar charts, heat maps, and dimensionality reduction plots of clustered data in FlowJo without the use of a plugin.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/mem\/\">MEM \u2013 Marker Enrichment Modeling (MEM)<\/a><\/strong>: Re-name clusters automatically and quantitatively based on their marker expression with a human- and machine-readable label.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/experiment-based-platforms\/plat-comp-overview\/cosine-similarity-matrix\/\">Spectral similarity scores<\/a><\/strong>: Calculate the cosine index for acquired data to evaluate reagent choices made in panel design based on data from your specific instrument and experimental conditions.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/graphs-and-gating\/advanced-gates\/auto-merged-quad-gate\/\">Auto-Quad gates<\/a><\/strong>: Automatically create quads and rectangle gates based on range gates, bi-sector gates or the data itself.<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/graphs-and-gating\/advanced-gates\/clone-gates\/\">Clone gates<\/a><\/strong>: Gates with the same name can now be linked together as \u2018clones\u2019 so that their position is synchronized. <\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/experiment-based-platforms\/plat-comp-overview\/autofluorescence-subtraction\/\">Autofluorescence extraction in traditional (gate-based) compensation<\/a><\/strong>: Use an unstained cell data file and true zero as the background value to model autofluorescence for extraction.<\/li>\n\n\n\n<li><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/r-tools-flowjo\/\"><strong>R-tools<\/strong><\/a> provide additional functionality for complex data analysis.&nbsp;<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/dimensionality-reduction\/\">Dimensionality reduction<\/a><\/strong> is a means of creating mathematically derived parameters that represent the collected parameters holistically, providing excellent visualization of high-dimensional data or clustering results.&nbsp;<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/taylor-index\/\">Taylor Index<\/a><\/strong>: A statistic used to asssess the goodness of a clustering result.<\/li>\n\n\n\n<li><strong><a href=\"http:\/\/\/sethduncan2.wpcomstaging.com\/advanced-features\/fj-commandline\/\">Command line<\/a>&nbsp;<\/strong> FlowJo is a means of running FlowJo &#8220;headlessly&#8221; without human intervention.<\/li>\n\n\n\n<li><strong><a href=\"http:\/\/\/sethduncan2.wpcomstaging.com\/advanced-features\/script-editor\/\">Script Editor<\/a><\/strong> is a tool that allow for users with JavaScript skills to interact programmatically with FlowJo to produce automation routines.&nbsp;<\/li>\n\n\n\n<li><strong><a href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/ddu\/\">De-identification utility<\/a><\/strong> is a stand-alone tool that allows users to strip identifying information out of FCS files to preserve privacy.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data.<\/p>\n","protected":false},"author":11,"featured_media":0,"parent":11495,"menu_order":54,"comment_status":"closed","ping_status":"closed","template":"home-flowjo.php","meta":{"footnotes":""},"tags":[20],"class_list":["post-13313","page","type-page","status-publish","hentry","tag-flowjo"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Advanced Features - FlowJo Documentation<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/docs.flowjo.com\/flowjo\/advanced-features\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta 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