{"id":360,"date":"2022-10-06T16:31:47","date_gmt":"2022-10-06T08:31:47","guid":{"rendered":"https:\/\/denglab.org.cn\/?page_id=360"},"modified":"2024-11-19T16:47:07","modified_gmt":"2024-11-19T08:47:07","slug":"resources","status":"publish","type":"page","link":"https:\/\/denglab.org.cn\/index.php\/resources\/","title":{"rendered":"Resources"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"360\" class=\"elementor elementor-360\">\n\t\t\t\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-ec23c80 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"ec23c80\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-55cf28e\" data-id=\"55cf28e\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-32c37d9 elementor-widget elementor-widget-heading\" data-id=\"32c37d9\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.6.7 - 03-07-2022 *\/\n.elementor-heading-title{padding:0;margin:0;line-height:1}.elementor-widget-heading .elementor-heading-title[class*=elementor-size-]>a{color:inherit;font-size:inherit;line-height:inherit}.elementor-widget-heading .elementor-heading-title.elementor-size-small{font-size:15px}.elementor-widget-heading .elementor-heading-title.elementor-size-medium{font-size:19px}.elementor-widget-heading .elementor-heading-title.elementor-size-large{font-size:29px}.elementor-widget-heading .elementor-heading-title.elementor-size-xl{font-size:39px}.elementor-widget-heading .elementor-heading-title.elementor-size-xxl{font-size:59px}<\/style><h2 class=\"elementor-heading-title elementor-size-default\">Deng Lab Supported Resources<\/h2>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-a71ab04 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"a71ab04\" data-element_type=\"section\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-c1d3241\" data-id=\"c1d3241\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-fbc3553 elementor-widget elementor-widget-toggle\" data-id=\"fbc3553\" data-element_type=\"widget\" data-widget_type=\"toggle.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.6.7 - 03-07-2022 *\/\n.elementor-toggle{text-align:left}.elementor-toggle .elementor-tab-title{font-weight:700;line-height:1;margin:0;padding:15px;border-bottom:1px solid #d4d4d4;cursor:pointer;outline:none}.elementor-toggle .elementor-tab-title .elementor-toggle-icon{display:inline-block;width:1em}.elementor-toggle .elementor-tab-title .elementor-toggle-icon svg{-webkit-margin-start:-5px;margin-inline-start:-5px;width:1em;height:1em}.elementor-toggle .elementor-tab-title .elementor-toggle-icon.elementor-toggle-icon-right{float:right;text-align:right}.elementor-toggle .elementor-tab-title .elementor-toggle-icon.elementor-toggle-icon-left{float:left;text-align:left}.elementor-toggle .elementor-tab-title .elementor-toggle-icon .elementor-toggle-icon-closed{display:block}.elementor-toggle .elementor-tab-title .elementor-toggle-icon .elementor-toggle-icon-opened{display:none}.elementor-toggle .elementor-tab-title.elementor-active{border-bottom:none}.elementor-toggle .elementor-tab-title.elementor-active .elementor-toggle-icon-closed{display:none}.elementor-toggle .elementor-tab-title.elementor-active .elementor-toggle-icon-opened{display:block}.elementor-toggle .elementor-tab-content{padding:15px;border-bottom:1px solid #d4d4d4;display:none}@media (max-width:767px){.elementor-toggle .elementor-tab-title{padding:12px}.elementor-toggle .elementor-tab-content{padding:12px 10px}}<\/style>\t\t<div class=\"elementor-toggle\" role=\"tablist\">\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2631\" class=\"elementor-tab-title\" data-tab=\"1\" role=\"tab\" aria-controls=\"elementor-tab-content-2631\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Denglab Metagenomic Analysis Pipeline (DMAP)<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2631\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"1\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2631\"><p>This analysis pipeline is built and maintained by Deng Lab and it is suitable for high-throughput sequencing data analysis, focusing on amplicon sequencing data (16S rRNA, ITS, 18S rRNA and functional genes).<\/p><p>This platform requires manual register. Please send your full name, affiliation and supervisor name to Prof. Ye Deng for registration.<\/p><p>Galaxy Platform page: <a href=\"https:\/\/dmap.denglab.org.cn\">https:\/\/dmap.denglab.org.cn<\/a><\/p><p>Citation: <span style=\"color: #3366ff;\">Kai Feng, Zhaojing Zhang, Weiwei Cai, Wenzong Liu, Meiying Xu, Huaqun Yin, Aijie Wang, Zhili He, Ye Deng. Biodiversity and species competition regulate the resilience of microbial biofilm community. Molecular Ecology 26 (2017) 6170-82. DOI:<a style=\"color: #3366ff;\" href=\"https:\/\/doi.org\/10.1111\/mec.14356\" target=\"_blank\" rel=\"noopener\">10.1111\/mec.14356<\/a><\/span><\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2632\" class=\"elementor-tab-title\" data-tab=\"2\" role=\"tab\" aria-controls=\"elementor-tab-content-2632\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">iNAP (integrated Network Analysis Pipeline)<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2632\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"2\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2632\"><p>This analysis pipeline is built and maintained by Metagenomics for Environmental Microbiology (MEM) (Deng Lab) and it is used to model, analyze and manage the the Molecular Ecological Networks (MENs) for adjacent matrix and Inter-Domain Ecological Networks (IDENs) for bipartite matrix from metagenomic datasets, e.g. GeoChip and Sequencing, and synchronous plant surveys, including Molecular Ecological Network Analysis (MENA) Pipeline and InterDomain Ecological Network Analysis Pipeline (IDENAP).<\/p><p>This platform is registry-open.<\/p><p>Galaxy Platform page: <a href=\"https:\/\/inap.denglab.org.cn\">https:\/\/inap.denglab.org.cn<\/a><\/p><p>Citation: <span style=\"color: #3366ff;\"><a style=\"color: #3366ff;\">Kai Feng, Xi Peng, Zheng Zhang, Songsong Gu, Qing He, Wenli Shen, Zhujun Wang, Danrui Wang, Qiulong Hu, Yan Li, Shang Wang, Ye Deng. iNAP: an integrated Network Analysis Pipeline for microbiome studies. iMeta. 2022,1:e13.\u00a0<\/a><a style=\"color: #3366ff;\" href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/imt2.13\" target=\"_new\">https:\/\/doi.org\/10.1002\/imt2.13<\/a><\/span><\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2633\" class=\"elementor-tab-title\" data-tab=\"3\" role=\"tab\" aria-controls=\"elementor-tab-content-2633\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Rapid DEgenerate Primer design program<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2633\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"3\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2633\"><p>This analysis pipeline is built by Deng Lab. It is used for sequence database management and primer assessment.<\/p><p>Galaxy Platform page: <a href=\"https:\/\/ardep.denglab.org.cn\">https:\/\/ardep.denglab.org.cn<\/a><\/p><p>Citation: <span style=\"color: #3366ff;\">Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang, Ye Deng*. ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies. International Journal of Environmental Research and Public Health, 2020, 17: 5958. DOI:<a style=\"color: #3366ff;\" href=\"https:\/\/doi.org\/10.3390\/ijerph17165958\" target=\"_blank\" rel=\"noopener\">10.3390\/ijerph17165958<\/a><\/span><\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2634\" class=\"elementor-tab-title\" data-tab=\"4\" role=\"tab\" aria-controls=\"elementor-tab-content-2634\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Antibiotic Resistance Gene Analyzer (ARGA)<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2634\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"4\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2634\"><p>This pipeline is used for antibiotic resistance genes (ARGs) analysis based on the Sequence Database for ARGs (SDARG).<\/p><p>Galaxy Platform page: <a href=\"https:\/\/arga.denglab.org.cn\">https:\/\/arga.denglab.org.cn<\/a><\/p><p>Citation: <span style=\"font-size: small;\"><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0160412019303745\" target=\"_blank\" rel=\"noopener\">Ziyan Wei, Yueni Wu, Kai Feng, Min Yang, Yu Zhang, Qichao Tu, Jun Wang and Ye Deng*. ARGA, a pipeline for primer evaluation on antibiotic resistance genes.\u00a0<i>Environment International<\/i>, 2019, 128: 137-145. https:\/\/doi.org\/10.1016\/j.envint.2019.04.030<\/a><\/span><\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2635\" class=\"elementor-tab-title\" data-tab=\"5\" role=\"tab\" aria-controls=\"elementor-tab-content-2635\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Nitrogen Cycling Functional Gene Analyzer (NcycFunGen)<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2635\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"5\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2635\"><p>This pipeline is used for nitrogen functional gene analysis based on the Sequence Database for NcycFunGen.<\/p><p>Galaxy Platform page: <a href=\"https:\/\/ncycfungen.denglab.org.cn\">https:\/\/ncycfungen.denglab.org.cn<\/a><\/p><p>Citation: <span style=\"color: #3366ff;\">Zhujun Wang,Kai Feng,Ziyan Wei,Yueni Wu,Kazuo Isobe,Keishi Senoo,Xi Peng,Danrui Wang,Qing He,Xiongfeng Du,Shuzhen Li,Yan Li,Ye Deng*, 2022, Methods in Ecology and Evolution. doi: <a class=\"epub-doi\" style=\"color: #3366ff;\" href=\"https:\/\/doi.org\/10.1111\/2041-210X.13946\" aria-label=\"Digital Object Identifier\">ttps:\/\/doi.org\/10.1111\/2041-210X.13946<\/a><\/span><\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t<div class=\"elementor-toggle-item\">\n\t\t\t\t\t<div id=\"elementor-tab-title-2636\" class=\"elementor-tab-title\" data-tab=\"6\" role=\"tab\" aria-controls=\"elementor-tab-content-2636\" aria-expanded=\"false\">\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon elementor-toggle-icon-left\" aria-hidden=\"true\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-closed\"><i class=\"fas fa-caret-right\"><\/i><\/span>\n\t\t\t\t\t\t\t\t<span class=\"elementor-toggle-icon-opened\"><i class=\"elementor-toggle-icon-opened fas fa-caret-up\"><\/i><\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t\t\t<a href=\"\" class=\"elementor-toggle-title\">Reprogrammed Expectation Maximization Iterative Reconstruction of Genes from the Environment (REMIRGE)<\/a>\n\t\t\t\t\t<\/div>\n\n\t\t\t\t\t<div id=\"elementor-tab-content-2636\" class=\"elementor-tab-content elementor-clearfix\" data-tab=\"6\" role=\"tabpanel\" aria-labelledby=\"elementor-tab-title-2636\"><p>It is used for reconstruct full-length functional(or ribosomal) genes from microbial community short read sequencing data.<\/p><p>Galaxy Platform page: <a href=\"https:\/\/remirge.denglab.org.cn\">https:\/\/remirge.denglab.org.cn<\/a><\/p><p>\u00a0<\/p><\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Deng Lab Supported Resources Denglab Metagenomic Analysis Pipeline (DMAP) This analysis pipeline is \u2026<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-360","page","type-page","status-publish","hentry"],"blocksy_meta":{"styles_descriptor":{"styles":{"desktop":"","tablet":"","mobile":""},"google_fonts":[],"version":5}},"_links":{"self":[{"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/pages\/360","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/comments?post=360"}],"version-history":[{"count":20,"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/pages\/360\/revisions"}],"predecessor-version":[{"id":714,"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/pages\/360\/revisions\/714"}],"wp:attachment":[{"href":"https:\/\/denglab.org.cn\/index.php\/wp-json\/wp\/v2\/media?parent=360"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}