{"id":414,"date":"2021-11-23T12:40:12","date_gmt":"2021-11-23T11:40:12","guid":{"rendered":"https:\/\/grupos.eez.csic.es\/mae\/?p=414"},"modified":"2022-09-20T12:58:39","modified_gmt":"2022-09-20T10:58:39","slug":"script-for-microbiome-analysis","status":"publish","type":"post","link":"https:\/\/grupos.eez.csic.es\/mae\/script-for-microbiome-analysis\/","title":{"rendered":"Script for microbiome analysis"},"content":{"rendered":"\n<p>A package has been created in order to record R functions we usually use in our laboratory for the analysis of amplicon data. Alongside this package, a tutorial was made to show the main utilities of this package, as well as to make public our main workflow (<a href=\"https:\/\/nuriamw.github.io\/micro4all\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/nuriamw.github.io\/micro4all\/<\/a>). We cover several steps, including:<\/p>\n\n\n\n<p>1. &nbsp;Produce an amplicon sequence variant (ASV) table, making use of dada2 package.<\/p>\n\n\n\n<p>2. Study microbial diversity (\u03b1 and \u03b2 diversity).<\/p>\n\n\n\n<p>3. Get taxonomical profiles at <em>phylum<\/em> and <em>genus<\/em> level.<\/p>\n\n\n\n<p>4. Differential abundance analysis with ANCOMBC package.<\/p>\n\n\n\n<p>5. Ordination graphics and environmental fitting of soil physicochemical parameters.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A package has been created in order to record R functions we usually use in our laboratory for the analysis of amplicon data. Alongside this package, a tutorial was made to show the main utilities of this package, as well as to make public our main workflow (https:\/\/nuriamw.github.io\/micro4all\/). We cover several steps, including: 1. &nbsp;Produce [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":415,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"default","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"default","adv-header-id-meta":"","stick-header-meta":"default","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"categories":[1],"tags":[],"uagb_featured_image_src":{"full":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis.jpg",866,785,false],"thumbnail":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis-150x150.jpg",150,150,true],"medium":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis-300x272.jpg",300,272,true],"medium_large":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis-768x696.jpg",768,696,true],"large":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis.jpg",866,785,false],"1536x1536":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis.jpg",866,785,false],"2048x2048":["https:\/\/grupos.eez.csic.es\/mae\/wp-content\/uploads\/2021\/11\/mae-script-for-microbial-analysis.jpg",866,785,false]},"uagb_author_info":{"display_name":"admin-mae","author_link":"https:\/\/grupos.eez.csic.es\/mae\/author\/admin-mae\/"},"uagb_comment_info":2,"uagb_excerpt":"A package has been created in order to record R functions we usually use in our laboratory for the analysis of amplicon data. Alongside this package, a tutorial was made to show the main utilities of this package, as well as to make public our main workflow (https:\/\/nuriamw.github.io\/micro4all\/). We cover several steps, including: 1. &nbsp;Produce&hellip;","_links":{"self":[{"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/posts\/414"}],"collection":[{"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/comments?post=414"}],"version-history":[{"count":1,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/posts\/414\/revisions"}],"predecessor-version":[{"id":416,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/posts\/414\/revisions\/416"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/media\/415"}],"wp:attachment":[{"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/media?parent=414"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/categories?post=414"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/grupos.eez.csic.es\/mae\/wp-json\/wp\/v2\/tags?post=414"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}