{"id":2607,"date":"2023-09-11T21:42:44","date_gmt":"2023-09-11T12:42:44","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=2607"},"modified":"2024-01-13T01:23:35","modified_gmt":"2024-01-12T16:23:35","slug":"installation-of-lefse","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/installation-of-lefse\/","title":{"rendered":"Installation of LEfSe"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">LEfSe (Linear discriminant analysis Effect Size)\ub294 \ud1b5\uacc4 \ubd84\uc11d\uc744 \ud1b5\ud574 \ud2b9\uc815 class\uc640 \uad00\ub828\uc788\ub294 feature\ub97c \ucc3e\ub294 \ubc29\ubc95\uc774\ub2e4. Conda\ub97c \uc774\uc6a9\ud574 \uac04\ub2e8\ud558\uac8c \uc124\uce58\ud560 \uc218 \uc788\uc5b4\uc57c \ud558\ub098, library version \ucc28\uc774\ub85c \uc778\ud574 \uc124\uce58\uac00 \uc6d0\ud65c\ud788 \ub418\uc9c0 \uc54a\ub294 \uacbd\uc6b0\uac00 \ubc1c\uc0dd\ud55c\ub2e4. \uc5ec\uae30\uc11c\ub294 <\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-wp-embed is-provider-the-huttenhower-lab wp-block-embed-the-huttenhower-lab\"><div class=\"wp-block-embed__wrapper\">\n<blockquote class=\"wp-embedded-content\" data-secret=\"kyxdN9tIW2\"><a href=\"https:\/\/huttenhower.sph.harvard.edu\/lefse\/\">lefse<\/a><\/blockquote><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; clip: rect(1px, 1px, 1px, 1px);\" title=\"&#8220;lefse&#8221; &#8212; The Huttenhower Lab\" src=\"https:\/\/huttenhower.sph.harvard.edu\/lefse\/embed\/#?secret=y14Ly653xg#?secret=kyxdN9tIW2\" data-secret=\"kyxdN9tIW2\" width=\"500\" height=\"282\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe>\n<\/div><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\">Installation (conda)<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">\uc544\ub798 \uba85\ub839\uc5b4 \uc2e4\ud589\uc744 \ud1b5\ud574 LEfSe\ub97c \uc124\uce58\ud55c\ub2e4. \ub2e4\ub9cc, \uc544\ub798 \uc124\uce58\ub294 \ub9e4\uc6b0 \uc81c\ud55c\uc801\uc778 \uc2dc\uc2a4\ud15c\uc5d0\uc11c \ud14c\uc2a4\ud2b8\ud55c \uacb0\uacfc\ub85c, \uc77c\ubd80 \uc2dc\uc2a4\ud15c\uc5d0\uc11c\ub294 \uc815\uc0c1\uc801\uc73c\ub85c \uc124\uce58\ub418\uc9c0 \uc54a\uc744 \uc218\ub3c4 \uc788\ub2e4. <\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">conda create -n lefse python=2.7\nconda activate lefse\nconda install bioconda::lefse -y<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">wget --no-check-certificate https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/09\/environment.yml\nconda env create -f environment.yml<\/code><\/pre>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-4c538292-1193-4042-8001-ad463324ad14\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/09\/environment.yml\">environment<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/09\/environment.yml\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-4c538292-1193-4042-8001-ad463324ad14\">Download<\/a><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">(Optional) \uae30\uc874 \ud658\uacbd \uc0ad\uc81c\ud558\uae30<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">lefse \ud658\uacbd\uc774 \uc874\uc7ac\ud558\ub294 \uacbd\uc6b0, \uc544\ub798 \uba85\ub839\uc744 \ud1b5\ud574 \ud658\uacbd\uc744 \uc0ad\uc81c\ud55c\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">conda env remove -n lefse<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\uc0ac\uc6a9 \ud14c\uc2a4\ud2b8<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">SegataLab\uc758 GitHub example code\ub97c \uc774\uc6a9\ud574 \uc815\uc0c1 \uc124\uce58 \uc5ec\ubd80\ub97c \ud655\uc778\ud55c\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><a href=\"https:\/\/github.com\/SegataLab\/lefse\/blob\/master\/example\/bioconda-lefse_run.sh\">https:\/\/github.com\/SegataLab\/lefse\/blob\/master\/example\/bioconda-lefse_run.sh<\/a><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"bash\" class=\"language-bash\">conda activate lefse\nwget https:\/\/github.com\/biobakery\/biobakery\/raw\/master\/test_suite\/biobakery_tests\/data\/lefse\/input\/hmp_small_aerobiosis.txt -O hmp_aerobiosis_small.txt\nlefse_format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000\nlefse_run.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res\nlefse_plot_res.py hmp_aerobiosis_small.res hmp_aerobiosis_small.png\nlefse_plot_cladogram.py hmp_aerobiosis_small.res hmp_aerobiosis_small.cladogram.png --format png\nmkdir biomarkers_raw_images\nlefse_plot_features.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res biomarkers_raw_images\/\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\">##<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Introduction LEfSe (Linear discriminant analysis Effect Size)\ub294 \ud1b5\uacc4 \ubd84\uc11d\uc744 \ud1b5\ud574 \ud2b9\uc815 class\uc640 \uad00\ub828\uc788\ub294 feature\ub97c \ucc3e\ub294 \ubc29\ubc95\uc774\ub2e4. Conda\ub97c \uc774\uc6a9\ud574 \uac04\ub2e8\ud558\uac8c \uc124\uce58\ud560 \uc218 \uc788\uc5b4\uc57c \ud558\ub098, library version \ucc28\uc774\ub85c \uc778\ud574 \uc124\uce58\uac00 \uc6d0\ud65c\ud788 \ub418\uc9c0 \uc54a\ub294 \uacbd\uc6b0\uac00 \ubc1c\uc0dd\ud55c\ub2e4. \uc5ec\uae30\uc11c\ub294 Installation (conda) \uc544\ub798 \uba85\ub839\uc5b4 \uc2e4\ud589\uc744 \ud1b5\ud574 LEfSe\ub97c \uc124\uce58\ud55c\ub2e4. \ub2e4\ub9cc, \uc544\ub798 \uc124\uce58\ub294 \ub9e4\uc6b0 \uc81c\ud55c\uc801\uc778 \uc2dc\uc2a4\ud15c\uc5d0\uc11c \ud14c\uc2a4\ud2b8\ud55c \uacb0\uacfc\ub85c, \uc77c\ubd80 \uc2dc\uc2a4\ud15c\uc5d0\uc11c\ub294 \uc815\uc0c1\uc801\uc73c\ub85c \uc124\uce58\ub418\uc9c0 \uc54a\uc744 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","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":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","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":"","_members_access_role":[],"_members_access_error":""},"categories":[20,1],"tags":[],"class_list":["post-2607","post","type-post","status-publish","format-standard","hentry","category-tools","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Installation of LEfSe - Biomedical Data Science Laboratory<\/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:\/\/bdsl.jbnu.ac.kr\/blog\/installation-of-lefse\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Installation of LEfSe - Biomedical Data Science Laboratory\" \/>\n<meta property=\"og:description\" content=\"Introduction LEfSe (Linear discriminant analysis Effect Size)\ub294 \ud1b5\uacc4 \ubd84\uc11d\uc744 \ud1b5\ud574 \ud2b9\uc815 class\uc640 \uad00\ub828\uc788\ub294 feature\ub97c \ucc3e\ub294 \ubc29\ubc95\uc774\ub2e4. Conda\ub97c \uc774\uc6a9\ud574 \uac04\ub2e8\ud558\uac8c \uc124\uce58\ud560 \uc218 \uc788\uc5b4\uc57c \ud558\ub098, library version \ucc28\uc774\ub85c \uc778\ud574 \uc124\uce58\uac00 \uc6d0\ud65c\ud788 \ub418\uc9c0 \uc54a\ub294 \uacbd\uc6b0\uac00 \ubc1c\uc0dd\ud55c\ub2e4. \uc5ec\uae30\uc11c\ub294 Installation (conda) \uc544\ub798 \uba85\ub839\uc5b4 \uc2e4\ud589\uc744 \ud1b5\ud574 LEfSe\ub97c \uc124\uce58\ud55c\ub2e4. \ub2e4\ub9cc, \uc544\ub798 \uc124\uce58\ub294 \ub9e4\uc6b0 \uc81c\ud55c\uc801\uc778 \uc2dc\uc2a4\ud15c\uc5d0\uc11c \ud14c\uc2a4\ud2b8\ud55c \uacb0\uacfc\ub85c, \uc77c\ubd80 \uc2dc\uc2a4\ud15c\uc5d0\uc11c\ub294 \uc815\uc0c1\uc801\uc73c\ub85c \uc124\uce58\ub418\uc9c0 \uc54a\uc744 [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/installation-of-lefse\/\" \/>\n<meta property=\"og:site_name\" content=\"Biomedical Data Science Laboratory\" \/>\n<meta property=\"article:published_time\" content=\"2023-09-11T12:42:44+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-01-12T16:23:35+00:00\" \/>\n<meta name=\"author\" content=\"sphong\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"sphong\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/\"},\"author\":{\"name\":\"sphong\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/#\\\/schema\\\/person\\\/8d22f775fcc218b1184ec0d890034e9b\"},\"headline\":\"Installation of LEfSe\",\"datePublished\":\"2023-09-11T12:42:44+00:00\",\"dateModified\":\"2024-01-12T16:23:35+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/\"},\"wordCount\":43,\"commentCount\":0,\"publisher\":{\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/#organization\"},\"articleSection\":[\"Tools\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/\",\"url\":\"https:\\\/\\\/bdsl.jbnu.ac.kr\\\/blog\\\/installation-of-lefse\\\/\",\"name\":\"Installation of LEfSe - 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