{"id":1884,"date":"2022-05-25T22:25:58","date_gmt":"2022-05-25T22:25:58","guid":{"rendered":"https:\/\/eccb2022.org\/?page_id=1884"},"modified":"2022-07-04T15:01:54","modified_gmt":"2022-07-04T15:01:54","slug":"ntb-t02","status":"publish","type":"page","link":"https:\/\/eccb2022.org\/ntb-t02\/","title":{"rendered":"NTB-T02"},"content":{"rendered":"\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-6f6b038\" data-block-id=\"6f6b038\"><style>.stk-6f6b038 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><strong>Title<\/strong><\/span><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-ca77bb3\" data-block-id=\"ca77bb3\"><h3 class=\"stk-block-heading__text\">To rarefy or not to rarefy microbiome data? What are the alpha diversity metrics?<\/h3><\/div>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-77074a6\" data-block-id=\"77074a6\"><style>.stk-77074a6 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><strong><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><span style=\"color: var(--paletteColor4, #1a928e);\" class=\"stk-highlight\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\">Tutorial details<\/span><\/span><\/span><\/strong><\/span><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<ul><li>Date: Thursday, September 15th<\/li><li>Time: 17:00 to 20:00 CEST<\/li><li>Format: Virtual<\/li><\/ul>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-0994530\" data-block-id=\"0994530\"><style>.stk-0994530 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\">Instructors<\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<ul><li><strong>Violeta Larios-Serrato<\/strong>, Winter Genomics (M\u00e9xico)<\/li><li><strong>Maira Nayeli Luis-Vargas<\/strong>, Winter Genomics (M\u00e9xico)<\/li><li><strong>Karla Ruiz<\/strong>, Winter Genomics (M\u00e9xico)<\/li><li><strong>Kenya Contreras<\/strong>, Winter Genomics (M\u00e9xico)&nbsp;\u2013 Helper<\/li><\/ul>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-0c3aa28\" data-block-id=\"0c3aa28\"><style>.stk-0c3aa28 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\">Summary<\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<p>This tutorial will cover the essential aspects of the microbiome alpha diversity: rarefaction and some alpha diversity metrics. Alpha diversity measures the microbiome diversity in individual samples. However, some other metrics (i.e. Shannon, Inverse Simpson and Pielou) are used to study the different properties of the microbiome communities. We will use R and Rstudio to learn and identify whether to rarefy and calculate other metrics to compare samples (richness, diversity, dominance) and plot the results in great charts.<\/p>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-4a8e43e\" data-block-id=\"4a8e43e\"><style>.stk-4a8e43e .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><strong>Intended audience<\/strong><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<p>Life sciences professionals interested in microbiome 16S and\/or metabarcoding projects.<\/p>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-4cdfd01\" data-block-id=\"4cdfd01\"><style>.stk-4cdfd01 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><strong>Prerequisites<\/strong><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<ul><li>Basic knowledge of R and RStudio, like data frames, file import and package installation.&nbsp;<\/li><li>Basic principles of sequencing.<\/li><\/ul>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-cdd954b\" data-block-id=\"cdd954b\"><style>.stk-cdd954b .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><strong>Maximum number of attendees<\/strong><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<p>20<\/p>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-1689a19\" data-block-id=\"1689a19\"><style>.stk-1689a19 .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><strong><strong>Material required (for participants)<\/strong><\/strong><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<p>R and RStudio (at least 4.0 version) should be installed. Attendees will need a desktop or laptop computer (not tablets or notebook-type laptops) with at least 4 GB RAM.&nbsp;<\/p>\n\n\n\n<div class=\"wp-block-stackable-heading stk-block-heading stk-block stk-38c235b\" data-block-id=\"38c235b\"><style>.stk-38c235b .stk-block-heading__bottom-line{height:1px !important;background-color:var(u002du002dpaletteColor2,#f7b032) !important;margin-top:12px !important}<\/style><h5 class=\"stk-block-heading__text\"><strong>Programme<\/strong><\/h5><div class=\"stk-block-heading__bottom-line\"><\/div><\/div>\n\n\n\n<ul class=\"oculto\"><li><strong>Project description<\/strong>: in this topic, we will explain how a 16S rRNA microbiome project is performed, starting from the experimental part to the bioinformatic data analysis. (15 min)<\/li><li><strong>File import<\/strong>: the student will learn how to import datasets that will be used during the workshop. (15 min)<\/li><li><strong>Rarefaction<\/strong>: explanation of what rarefaction is, how the algorithm works and its implications in microbiome 16S rRNA analyses. We will construct a rarefaction curve of the data using R programming language. (1h)<\/li><li><strong>Alpha diversity<\/strong> <strong>index<\/strong>: creation of the following graphs that are commonly used that facilitate the analysis of 16S microbiome data (1.5h)<ul><li>Dot plots<\/li><li>Box plots<\/li><li>Alpha diversity metrics (Shannon, Simpson, Pielou)<\/li><li>Hypothesis tests<\/li><\/ul><\/li><\/ul>\n\n\n\n<figure class=\"wp-block-table tabla-ntb is-style-regular\" style=\"font-size:15px\"><table><thead><tr><th class=\"has-text-align-left\" data-align=\"left\"> <strong>T<\/strong>IME<\/th><th class=\"has-text-align-left\" data-align=\"left\"><strong>CONTENT<\/strong><\/th><\/tr><\/thead><tbody><tr><td class=\"has-text-align-left\" data-align=\"left\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><strong>17:00 &#8211; 17:15<\/strong><\/span><\/td><td class=\"has-text-align-left\" data-align=\"left\"><strong>Project description<\/strong>. In this topic, we will explain how a 16S rRNA microbiome project is performed, starting from the experimental part to the bioinformatic data analysis<\/td><\/tr><tr><td class=\"has-text-align-left\" data-align=\"left\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><strong>17:<\/strong><\/span><span style=\"\" class=\"stk-highlight\"><strong style=\"color: var(--paletteColor4, #0081a7);\">15 &#8211; 17:30<\/strong><\/span><\/td><td class=\"has-text-align-left\" data-align=\"left\"><strong>File import. <\/strong>The student will learn how to import datasets that will be used during the workshop<\/td><\/tr><tr><td class=\"has-text-align-left\" data-align=\"left\"><strong><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\">17:30 &#8211; 18:30<\/span><\/strong> <\/td><td class=\"has-text-align-left\" data-align=\"left\"><strong>Rarefaction<\/strong>. Explanation of what rarefaction is, how the algorithm works and its implications in microbiome 16S rRNA analyses. We will construct a rarefaction curve of the data using R programming language<\/td><\/tr><tr><td class=\"has-text-align-left\" data-align=\"left\"><span style=\"color: var(--paletteColor4, #0081a7);\" class=\"stk-highlight\"><strong>18:30 &#8211; 20:00<\/strong><\/span><\/td><td class=\"has-text-align-left\" data-align=\"left\"><strong>Alpha diversity<\/strong>. Creation of the following graphs that are commonly used that facilitate the analysis of 16S microbiome data:<br>&#8211; Dot plots <br>&#8211; Box plots<br>&#8211; Alpha diversity metrics (Shannon, Simpson, Pielou)<br>&#8211; Hypothesis tests<br><\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>Title To rarefy or not to rarefy microbiome data? What are the alpha diversity metrics? Tutorial details Date: Thursday, September 15th Time: 17:00 to 20:00 CEST Format: Virtual Instructors Violeta Larios-Serrato, Winter Genomics (M\u00e9xico) Maira Nayeli Luis-Vargas, Winter Genomics (M\u00e9xico) Karla Ruiz, Winter Genomics (M\u00e9xico) Kenya Contreras, Winter Genomics (M\u00e9xico)&nbsp;\u2013 Helper Summary This tutorial will cover the essential aspects of the microbiome alpha diversity: rarefaction and some alpha diversity metrics. Alpha diversity measures the microbiome diversity in individual samples. However, some other metrics (i.e. Shannon, Inverse Simpson and Pielou) are used to study the different properties of the microbiome communities.\u2026<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"blocksy_meta":{"styles_descriptor":{"styles":{"desktop":"","tablet":"","mobile":""},"google_fonts":[],"version":4},"page_title_panel":"","has_hero_section":"default","7b9ded946d4680066060ddae606a4869":"","hero_section":"type-1","hero_elements":[{"id":"custom_title","enabled":true,"heading_tag":"h1","title":"Inicio"},{"id":"custom_description","enabled":true,"description_visibility":{"desktop":true,"tablet":true,"mobile":false}},{"id":"custom_meta","enabled":false,"meta_elements":[{"id":"author","enabled":true,"label":"Por","has_author_avatar":"yes","avatar_size":25},{"id":"post_date","enabled":true,"label":"El","date_format_source":"default","date_format":"M j, 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0.04)"}},"boxed_content_spacing":{"desktop":{"top":"40px","bottom":"40px","left":"40px","right":"40px","linked":true},"tablet":{"top":"35px","bottom":"35px","left":"35px","right":"35px","linked":true},"mobile":{"top":"20px","bottom":"20px","left":"20px","right":"20px","linked":true}},"content_boxed_radius":{"top":"3px","bottom":"3px","left":"3px","right":"3px","linked":true},"c17a8304e5e66c0922c2d4f80257a4e2":"","disable_featured_image":"no","disable_share_box":"no","disable_header":"no","disable_footer":"no"},"featured_image_urls":{"full":"","thumbnail":"","medium":"","medium_large":"","large":"","1536x1536":"","2048x2048":""},"post_excerpt_stackable":"<p>Title To rarefy or not to rarefy microbiome data? What are the alpha diversity metrics? Tutorial details Date: Thursday, September 15thTime: 17:00 to 20:00 CESTFormat: Virtual Instructors Violeta Larios-Serrato, Winter Genomics (M\u00e9xico)Maira Nayeli Luis-Vargas, Winter Genomics (M\u00e9xico)Karla Ruiz, Winter Genomics (M\u00e9xico)Kenya Contreras, Winter Genomics (M\u00e9xico)&nbsp;\u2013 Helper Summary This tutorial will cover the essential aspects of the microbiome alpha diversity: rarefaction and some alpha diversity metrics. Alpha diversity measures the microbiome diversity in individual samples. However, some other metrics (i.e. Shannon, Inverse Simpson and Pielou) are used to study the different properties of the microbiome communities. We will use R and&hellip;<\/p>\n","category_list":"","author_info":{"name":"victorcuencaharo","url":"https:\/\/eccb2022.org\/author\/victorcuencaharo\/"},"comments_num":"0 comments","_links":{"self":[{"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/pages\/1884"}],"collection":[{"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/comments?post=1884"}],"version-history":[{"count":40,"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/pages\/1884\/revisions"}],"predecessor-version":[{"id":2464,"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/pages\/1884\/revisions\/2464"}],"wp:attachment":[{"href":"https:\/\/eccb2022.org\/wp-json\/wp\/v2\/media?parent=1884"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}