RRID | Searching in Community Resources

<!DOCTYPE html>    <html lang="en">  <head> <title>RRID | Searching in Community Resources</title>  <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="description" content="Results for the query '*' in resources across SciCrunch: Registry"> <meta name="author" content=""> <meta name="google-site-verification" content="vhe7FXQ5uQHNwM10raiS4rO23GgbFW6-iyRfapxGPJc" />  <link rel="shortcut icon" href="/favicon.ico">  <link rel="stylesheet" href="/css/main.css"> <link rel="stylesheet" href="/assets/plugins/bootstrap/css/bootstrap.min.css"> <link rel="stylesheet" href="/assets/plugins/sky-forms/version-2.0.1/css/custom-sky-forms.css"> <link rel="stylesheet" href="/assets/css/style.css">  <link rel="stylesheet" href="/assets/plugins/line-icons/line-icons.css"> <link rel="stylesheet" href="/assets/plugins/font-awesome/css/font-awesome.min.css"> <link rel="stylesheet" href="/assets/plugins/owl-carousel/owl-carousel/owl.carousel.css">  <link rel="stylesheet" href="/assets/css/pages/page_search_inner.css"> <link rel="stylesheet" href="/assets/css/pages/page_search_inner_tables.css"> <link rel="stylesheet" href="/assets/plugins/scrollbar/src/perfect-scrollbar.css">  <link rel="stylesheet" href="/assets/css/themes/default.css" id="style_color"> <link rel="stylesheet" href="/assets/css/pages/page_log_reg_v2.css"> <link rel="stylesheet" href="/assets/css/shop/shop.blocks.css">  <link rel="stylesheet" href="/assets/css/custom.css"> <link rel="stylesheet" href="/css/community-search.css"> <link rel="stylesheet" href="/css/joyride-2.0.3.css"> <link rel="stylesheet" href="/js/Highcharts-6.0.7/code/css/highcharts.css"> <script type="text/javascript" src="/assets/plugins/jquery-3.4.1.min.js"></script> <script type="text/javascript" src="/js/main.js"></script> <script src="/js/angular-1.7.9/angular.min.js"></script> <script src="/js/ui-bootstrap-tpls-2.5.0.min.js"></script> <script src="/js/angular-1.7.9/angular-sanitize.js"></script> <script src="/js/module-error.js"></script> <script src="/js/module-resource.js"></script>  <style> #loading { background: #F7F7FF; display: none; } .page-overlay { width: 100%; height: 100%; z-index: 1000; top: 0; left: 0; position: fixed; } #restarting-warning { background: #FFF7F7; display: none; } #try-again-later-warning { display: none; } .center-style-1 { display: table; position: absolute; height: 100%; width: 100%; } .center-style-2 { display: table-cell; vertical-align: middle; } .center-style-3 { margin-left: auto; margin-right: auto; } </style> <script> window.page_loaded = false; function pageLoad() { document.getElementById("loading").style.display = "none"; document.getElementById("full-page").style.display = "block"; window.page_loaded = window.okSearchStatus; clearTimeout(window.reloadTimeout); checkReloadSearchPage(); } function checkReloadSearchPage() { document.getElementById("loading").style.display = "none"; document.getElementById("full-page").style.display = "block"; if(!window.page_loaded) { if(window.location.search.indexOf("restarted") === -1) { document.getElementById("restarting-warning").style.display = "block"; setTimeout(function() { var sep = window.location.search.indexOf("?") === -1 ? "?" : "&"; // check if other get query params exist window.location = window.location.href + sep + "restarted"; }, 5000); } else { document.getElementById("try-again-later-warning").style.display = "block"; } } } window.reloadTimeout = setTimeout(checkReloadSearchPage, 65000); </script> </head> <body onload="pageLoad()"> <noscript> <div class="alert alert-danger"> This site relies heavily on JavaScript. Many functions will not work if you continue with JavaScript disabled. </div> </noscript> <div id="loading" class="page-overlay"> <div class="center-style-1"> <div class="center-style-2"> <div class="center-style-3"> <center> <h2>Searching across hundreds of databases <i class="fa fa-cog fa-spin"></i></h2> <img src="/images/scicrunch.png" style="height: 100px" /> </center> </div> </div> </div> </div> <div id="restarting-warning" class="page-overlay"> <div class="center-style-1"> <div class="center-style-2"> <div class="center-style-3"> <center> <h2>Our searching services are busy right now. Your search will reload in five seconds.</h2> </center> </div> </div> </div> </div> <div id="try-again-later-warning" class="alert alert-warning" role="alert"> Our searching services are busy right now. Please try again later. </div> <script>document.getElementById("loading").style.display = "block";</script> <div id="full-page"> <script>document.getElementById("full-page").style.display = "none";</script> <script> window.okSearchStatus = true</script> <div class="wrapper-background" style="overflow:auto ">  <style> .header .navbar-default .navbar-nav > li > a:hover, .header .navbar-default .navbar-nav > .active > a { color: #0095FE; border-bottom: solid 2px #0095FE; } .header .dropdown-menu { border-top: solid 2px #0095FE; } .header .navbar .nav > li > .search:hover { color: #0095FE; background: #f7f7f7; border-bottom-color: #0095FE; } .topbar .loginbar li a:hover { color: #0095FE; } .header .btn-u { background: #0095FE; } .header .btn-u:hover { background: #0095FE; } .header .container > .navbar-header, .header .container-fluid > .navbar-header, .header .container > .navbar-collapse, .header .container-fluid > .navbar-collapse { margin-bottom: -30px; } </style> <div class="header-v1" style="z-index:99"> <div class="topbar-v1 margin-bottom-20" > <div class="container"> <div class="row"> <div class="col-md-6"> </div> <div class="col-md-6"> <ul class="list-unstyled top-v1-data"> <script> (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-34153437-1', 'auto'); // scicrunch ga('create', '', 'auto', 'community'); // community ga('send', 'pageview'); ga('community.send', 'pageview'); </script>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-0347ER9L11"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-0347ER9L11'); </script> <li><a href="#" class="btn-login">Login</a></li> <li><a class="referer-link" href="/resources/join">Register</a></li>  </ul> </div> </div> </div> </div> </div> <div class="header ">  <div class="topbar"> <div class="container">   </div> </div>   <div class="navbar navbar-default" role="navigation" style="margin-bottom: 20px;"> <div class="container">  <div class="navbar-header"> <a class="navbar-brand" href="/resources"> <img class="community-logo" src="/upload/community-logo/rin-resources_69984.png"/> <span class="community-name">RRID Portal</span> </a> </div>  <div> <ul class="nav navbar-nav">  <li class="active dropdown"> <a href="javascript:void(0)" class="dropdown-toggle joyride-about" data-toggle="dropdown">About</a> <ul class="dropdown-menu"> <li><a href="/resources/about/Getting Started" target="_blank">Getting Started</a></li><li><a href="/resources/about/tips" target="_blank">Search Features and Tips</a></li><li><a href="/resources/about/guidelines" target="_blank">Resource Citation Guidelines</a></li><li><a href="/resources/about/community_authorities" target="_blank">Community Standard Authorities</a></li><li><a href="/resources/about/faqs" target="_blank">FAQs and Tutorials</a></li><li><a href="/resources/about/scibot" target="_blank">SciBot</a></li> <li ><a href="/resources/about/resource">Add a Resource</a></li> </ul> </li>    </ul> </div>  </div> </div>  </div>  <div class="container login-backing" style="display:none;position: fixed;left:0;top:0;width:100%;height:100%;z-index: 20000;background: rgba(0,0,0,.8)">  <form method="post" action="/forms/login.php?cid=510"> <div class="reg-block login-box"> <div class="login-backing close dark">X</div> <div class="reg-block-header"> <h2>Log in</h2> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-envelope"></i></span> <input type="text" class="form-control" name="email" placeholder="Email"> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-lock"></i></span> <input type="password" class="form-control" name="password" placeholder="Password"> </div> <a class="referer-link" href="/resources/join">Create an account</a><br/> <span class="simple-toggle login-backing" modal=".forgot-password" style="cursor:pointer;color:#72c02c" title="Forgot Password">Forgot password?</span><br/> <hr> <div class="row"> <div class="col-md-10 col-md-offset-1"> <button type="submit" class="btn-u btn-block">Log In</button> </div> </div> </div> </form>  </div> <div class="back-hide forgot-password no-padding"> <div class="close dark less-right">X</div> <div id="sky-form4" class="sky-form" novalidate="novalidate"> <header>Forgot Password</header> <fieldset> <p> If you have forgotten your password you can enter your email here and get a temporary password sent to your email. <div class="forgot-pw-container"> <form class="forgot-pw-form"> <div class="input-group"> <input type="text" class="form-control forgot-email" name="query" placeholder="Account Email"/> <span class="input-group-btn"> <button class="btn-u" type="submit">Send</button> </span> </div> </form> </div> </p> </fieldset> </div> </div> <div class="large-modal back-hide leave-comm"> <div class="close dark less-right">X</div> <h2>Leaving Community</h2> <p style="margin:20px 0"> Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community. </p> <div class="btn-u btn-u-default close-btn">No</div> <a class="btn-u btn-u-red" href="/forms/leave.php?cid=510">Yes</a> </div> <ol id="joyRideHeaderContent" style="display:none"> <li data-class="joyride-about" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>About</h2> <p> Find out information about this community and visit other pages within it. You can also add a resource to the community here. </p> </li> <li data-class="joyride-community-resources" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>Community Resources</h2> <p> Search through data specific to this community </p> </li> <li data-class="joyride-more-resources" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>More Resources</h2> <p> Search through all of SciCrunch's data. </p> </li> <li data-class="joyride-literature" data-text="Next" data-options="tipLocation:bottom;tipAnimation:fade"> <h2>Literature</h2> <p> Search through literature data. </p> </li> </ol> <script type="text/javascript"> $(function() { $(".tutorial-header-btn").click(function () { $("body").joyride(); $("body").joyride("destroy"); // joyride bug, when multiple joyrides on a page $(".joyride-next-tip").show(); $("#joyRideHeaderContent").joyride( { "postStepCallback": function(index, tip) { }, "startOffset": 0, "tip_class": false, } ); }); }); </script> <div class="container login-backing" style="display:none;position: fixed;left:0;top:0;width:100%;height:100%;z-index: 20000;background: rgba(0,0,0,.8)">  <form method="post" action="/forms/login.php?cid=510"> <div class="reg-block login-box"> <div class="login-backing close dark">X</div> <div class="reg-block-header"> <h2>Log in</h2> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-envelope"></i></span> <input type="text" class="form-control" name="email" placeholder="Email"> </div> <div class="input-group margin-bottom-20"> <span class="input-group-addon"><i class="fa fa-lock"></i></span> <input type="password" class="form-control" name="password" placeholder="Password"> </div> <a class="referer-link" href="/resources/join">Create an account</a><br/> <span class="simple-toggle login-backing" modal=".forgot-password" style="cursor:pointer;color:#72c02c" title="Forgot Password">Forgot password?</span><br/> <hr> <div class="row"> <div class="col-md-10 col-md-offset-1"> <button type="submit" class="btn-u btn-block">Log In</button> </div> </div> </div> </form>  </div> <div class="back-hide forgot-password no-padding"> <div class="close dark less-right">X</div> <div id="sky-form4" class="sky-form" novalidate="novalidate"> <header>Forgot Password</header> <fieldset> <p> If you have forgotten your password you can enter your email here and get a temporary password sent to your email. <div class="forgot-pw-container"> <form class="forgot-pw-form"> <div class="input-group"> <input type="text" class="form-control forgot-email" name="query" placeholder="Account Email"/> <span class="input-group-btn"> <button class="btn-u" type="submit">Send</button> </span> </div> </form> </div> </p> </fieldset> </div> </div> <script type="text/javascript" src="/js/facets-wordcloud30.js"></script> <script> document.categoryGraphData = null; </script> <link href="/css/rin.css" rel="stylesheet" /> <div class="rin"> <div class="report"> <div class="header-scicrunch"> <div class="container"> <div class="row"> <div> <h1 style="margin-top:10px"> Tools  <a target='_self' href='https://rrid.site/rin/rrids' class='btn btn-primary'><i class='fa fa-bars'></i> Select Another Resource Report Type</a> </h1> <ol class="breadcrumb"> <li> <a class="color-white " target="_self" href="https://rrid.site" > Home </a> </li> <li> <a class="color-white " target="_self" href="https://rrid.site/rin/rrids" > Resource Reports </a> </li> <li> <a class="color-white active" target="_self" > Tools </a> </li> </ol> </div> </div> </div> </div> <div class="header-background-resolver"></div> <div class="row"> <div class="container"> <div class="wrapper"> <div class="row"> <div class="col-md-12"> <div> <div class="row"> <div class="col-md-12"> <p style="margin-bottom: 0px" class="truncate-medium" id="sc-descr"><a href="https://scicrunch.org/scicrunch/about/sources/nlx_144509-1">SciCrunch Registry</a> is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to <a href="https://scicrunch.org/create/resource">register your resource</a>.</p> </div> <div class="col-md-12 results-number" style="margin-top:10px;"> <style> .search-block-v2 h2 { color: #585f69; } .search-block-v2 .form-submit-button { background: #0095FE; } .search-block-save-search-btn { background: #9B6BCC; color: #FFF; border-radius: 0; } .search-block-reset-search-btn { background-color: #408DC9; color: white; border-radius: 0; } </style> <div class="search-block-v2 " style="margin-bottom:10px"> <div class="container"> <div> <form class="page-search-form1 submit-class"> <div> <p class="search-section-header" style="display: inline-block">Search</p> <p style="display: inline-block">Type in a keyword to search</p> </div> <div class="input-group"> <span class="input-group-btn"> <div class="btn btn-info help-tooltip-btn" data-name="rin-search-tips.html"> <i class="fa fa-question-circle"></i> </div> </span> <input type="text" class="form-control searchbar" id="search-banner-input" name="l" value="*"> <input type="hidden" id="autoValues"/> <input type="hidden" class="title-input" value=""/> <input type="hidden" class="type-input" value="search"/> <input type="hidden" class="category-input" value="data"/> <input type="hidden" class="subcategory-input" value=""/> <input type="hidden" class="source-input" value="nlx_144509-1"/> <input type="hidden" class="search-community" value="resources"/> <input type="hidden" class="stripped-community" value=""/> <input type="hidden" class="data-sources" value=""/> <input type="hidden" class="results-types" value=""/> <div class="autocomplete_append auto" style="z-index:10"></div> <span class="input-group-btn"> <input type="submit" class="btn-u form-submit-button" type="button" value="Search" style="height:34px;" /> </span>  <span class="input-group-btn"> <div class="btn-group tut-saved" style="margin-left:20px"> <button type="button" class="btn dropdown-toggle search-block-save-search-btn" data-toggle="dropdown" title="Save your search to receive notifications when there are updates"> <i class="fa fa-floppy-o"></i> Save search </button> <ul class="dropdown-menu" role="menu" style="text-align: left"> <li><a href="javascript:void(0)" class="btn-login">Login to Save Searches</a></li> </ul> </div> <div class="btn-group tut-saved" style="margin-left:10px"> <a target="_self" href="https://rrid.site/data/source/nlx_144509-1/search?q=&l=" class="btn search-block-reset-search-btn"> <i class="fa fa-undo"></i> Reset search </a> </div> </span> </div> </form> </div> </div> </div> <script> $(function(){ var synonyms_checked_flag = false; var synonyms = "true"; if(synonyms == "true") synonyms_checked_flag = true; $('#ScheckBox').prop('checked', synonyms_checked_flag || false); }); $('#ScheckBox').on('change', function() { localStorage.checked = $(this).is(':checked'); if(localStorage.checked == "true") window.location = window.location.href.replace("&exclude=synonyms", ""); else window.location = window.location.href.replace("#", "&exclude=synonyms#"); }); $(function(){ var acronyms_checked_flag = false; var acronyms = "false"; if(acronyms == "true") acronyms_checked_flag = true; $('#AcheckBox').prop('checked', acronyms_checked_flag || false); }); $('#AcheckBox').on('change', function() { localStorage.checked = $(this).is(':checked'); if(localStorage.checked == "true") window.location = window.location.href.replace("#", "&include=acronyms#"); else window.location = window.location.href.replace("&include=acronyms", ""); }); </script> </div> </div> <div class="row"> <div class="col-md-2 hidden-xs related-search"> <div class="row" style="margin-top:10px"> <div class="col-md-12 col-sm-4"> <a href="javascript:void(0)" class="hidden-default-toggle"> Filter by records added date</a> <div class="hidden-default"> <input id="modified-date-picker30" style="color:black" /> <div class="btn-group"> <a href="javascript:void(0)" id="modified-date-picker-before"><button class="btn btn-default">Before</button></a> <a href="javascript:void(0)" id="modified-date-picker-after"><button class="btn btn-default">After</button></a> </div> </div> <style> .hidden-default { display: none; } </style> <script> $(function() { $("#modified-date-picker30").datepicker(); function modifiedDatePicker(action) { var time = $("#modified-date-picker30").datepicker("getDate"); time = $.datepicker.formatDate("yymmdd", time); if(time == "") return; var query = window.location.search.replace(/filter\[\]=(gte|lte):\d+&?/gi, "") .replace(/filter\[\]=(gte|lte):/gi, ""); if(query.includes("&changed")){ query = query.replace(/facet\[\]=([a-z|0-9|%]+)&?/gi, ""); query = query.replace("&changed", ""); } var path = window.location.pathname.replace(/page\/\d+\/search/, "search"); var fullpath = path + query; var query_delim = "&"; if(window.location.search === "") { query_delim = "?"; } var modified_fullpath = fullpath + query_delim + "filter[]=" + action + ":" + time; modified_fullpath = modified_fullpath.replace("&&", "&") .replace("?&", "?"); window.location.href = modified_fullpath; } $("#modified-date-picker-before").click(function() { modifiedDatePicker("lte"); }); $("#modified-date-picker-after").click(function() { modifiedDatePicker("gte"); }); $(".hidden-default-toggle").click(function() { $(".hidden-default").slideToggle(); }); }); </script> <br/> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&filter[]=gte:20241104">See new records</a> <hr /> <h3>Options</h3> <ul class="list-group"> <li class="list-group-item"><a href="#" class="btn-login">Log in for Collection Options</a></li> </ul> <hr class="hr-small" /> <h3>Current Facets and Filters</h3><ul class="list-unstyled"><li>Keywords:analysis (facet)<a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20"><i class="fa red-x fa-times-circle"></i></a></li><li>Funding Agency:nhgri (facet)<a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20"><i class="fa red-x fa-times-circle"></i></a></li><li>Funding Agency:bergen research foundation (facet)<a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20"><i class="fa red-x fa-times-circle"></i></a></li></ul><hr style="margin-top:10px;margin-bottom:15px;"/> <div> <h3>Facets</h3> <form class="multi-facets" url="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20"> <ul class="list-group sidebar-nav-v1" id="sidebar-nav"> <li class="list-group-item list-toggle" data-toggle="collapse" data-parent="#sidebar-nav" href="#collapse-Resource_Type"> <a href="javascript:void(0)">Resource Type</a> <ul id="collapse-Resource_Type" class="collapse"> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Asoftware%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="28" title="software resource"> software resource (28) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20processing%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="21" title="data processing software"> data processing soft... (21) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20processing%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Asoftware%20application" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="21" title="software application"> software application (21) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20application" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="19" title="data analysis software"> data analysis softwa... (19) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20analysis%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Asequence%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="9" title="sequence analysis software"> sequence analysis so... (9) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="sequence%20analysis%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aservice%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="7" title="service resource"> service resource (7) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="service%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Asoftware%20toolkit" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="7" title="software toolkit"> software toolkit (7) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="software%20toolkit" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aanalysis%20service%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="6" title="analysis service resource"> analysis service res... (6) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="analysis%20service%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aproduction%20service%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="6" title="production service resource"> production service r... (6) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="production%20service%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20analysis%20service" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="5" title="data analysis service"> data analysis servic... (5) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20analysis%20service" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20or%20information%20resource" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="4" title="data or information resource"> data or information ... (4) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20or%20information%20resource" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aimage%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="4" title="image analysis software"> image analysis softw... (4) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="image%20analysis%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aalignment%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="alignment software"> alignment software (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="alignment%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20access%20protocol" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="data access protocol"> data access protocol (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20access%20protocol" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adatabase" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="database"> database (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="database" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aweb%20service" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="web service"> web service (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="web%20service" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20management%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="1" title="data management software"> data management soft... (1) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20management%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Adata%20repository" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="1" title="data repository"> data repository (1) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="data%20repository" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Anetwork%20analysis%20software" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="1" title="network analysis software"> network analysis sof... (1) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="network%20analysis%20software" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Resource%20Type%3Aorganization%20portal" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="1" title="organization portal"> organization portal (1) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Resource%20Type" facet="organization%20portal" /> </div> </div> </li> </ul> </li> <li class="list-group-item list-toggle" data-toggle="collapse" data-parent="#sidebar-nav" href="#collapse-Keywords"> <a href="javascript:void(0)">Keywords</a> <ul id="collapse-Keywords" class="collapse"> <li style="border-top: 1px solid #ddd"> <a> analysis (32) </a> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Abio.tools" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="16" title="bio.tools"> bio.tools (16) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="bio.tools" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Adata" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="14" title="data"> data (14) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="data" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Agenome" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="9" title="genome"> genome (9) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="genome" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Agene" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="8" title="gene"> gene (8) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="gene" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Asequence" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="8" title="sequence"> sequence (8) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="sequence" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Aread" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="7" title="read"> read (7) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="read" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Asequencing" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="6" title="sequencing"> sequencing (6) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="sequencing" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Aalignment" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="5" title="alignment"> alignment (5) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="alignment" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Adna" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="5" title="dna"> dna (5) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="dna" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Aprotein" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="5" title="protein"> protein (5) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="protein" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Arna" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="5" title="rna"> rna (5) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="rna" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Aerror" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="4" title="error"> error (4) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="error" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Areference" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="4" title="reference"> reference (4) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="reference" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Acell" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="cell"> cell (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="cell" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Adatabase" style="width:90%;padding-right:30px;display:inline-block;border:0" data-count="3" title="database"> database (3) </a> <div class="pull-right"> <div class="checkbox"> <input type="checkbox" class="facet-checkbox" style="margin-top: 9px" column="Keywords" facet="database" /> </div> </div> </li> <li style="border-top: 1px solid #ddd"> <a href="https://rrid.site/data/source/nlx_144509-1/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&facet[]=Keywords%3Afunctional" 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Bowtie is short read aligner.</p> <p></p> <p> <strong>Proper citation:</strong> Bowtie (RRID:SCR_005476) <a href="javascript:void(0)" onclick="copyTextToClipboard('Bowtie (RRID:SCR_005476)', 'rrid:scr_005476')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_005476" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_013035/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_013035">TopHat <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_013035 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 5000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_013035&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://ccb.jhu.edu/software/tophat/index.shtml">http://ccb.jhu.edu/software/tophat/index.shtml <i class='fa fa-external-link'></i></a></p> <p>Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.</p> <p></p> <p> <strong>Proper citation:</strong> TopHat (RRID:SCR_013035) <a href="javascript:void(0)" onclick="copyTextToClipboard('TopHat (RRID:SCR_013035)', 'rrid:scr_013035')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_013035" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_018665/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_018665">QoRTs <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_018665 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_018665&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://hartleys.github.io/QoRTs/">https://hartleys.github.io/QoRTs/ <i class='fa fa-external-link'></i></a></p> <p>Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.</p> <p></p> <p> <strong>Proper citation:</strong> QoRTs (RRID:SCR_018665) <a href="javascript:void(0)" onclick="copyTextToClipboard('QoRTs (RRID:SCR_018665)', 'rrid:scr_018665')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_018665" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_018977/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_018977">GOnet <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_018977 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_018977&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://tools.dice-database.org/GOnet/)">http://tools.dice-database.org/GOnet/) <i class='fa fa-external-link'></i></a></p> <p>Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.</p> <p></p> <p> <strong>Proper citation:</strong> GOnet (RRID:SCR_018977) <a href="javascript:void(0)" onclick="copyTextToClipboard('GOnet (RRID:SCR_018977)', 'rrid:scr_018977')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_018977" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_018141/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_018141">ChromHMM <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_018141 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_018141&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://compbio.mit.edu/ChromHMM/">http://compbio.mit.edu/ChromHMM/ <i class='fa fa-external-link'></i></a></p> <p>Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.</p> <p></p> <p> <strong>Proper citation:</strong> ChromHMM (RRID:SCR_018141) <a href="javascript:void(0)" onclick="copyTextToClipboard('ChromHMM (RRID:SCR_018141)', 'rrid:scr_018141')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_018141" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016679/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016679">Pavian <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016679 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016679&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://github.com/fbreitwieser/pavian">https://github.com/fbreitwieser/pavian <i class='fa fa-external-link'></i></a></p> <p>Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.</p> <p></p> <p> <strong>Proper citation:</strong> Pavian (RRID:SCR_016679) <a href="javascript:void(0)" onclick="copyTextToClipboard('Pavian (RRID:SCR_016679)', 'rrid:scr_016679')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016679" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016652/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016652">fermi <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016652 </h4> </ul> </div>  <p><a target="_blank" href="https://github.com/lh3/fermi">https://github.com/lh3/fermi <i class='fa fa-external-link'></i></a></p> <p>Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.</p> <p></p> <p> <strong>Proper citation:</strong> fermi (RRID:SCR_016652) <a href="javascript:void(0)" onclick="copyTextToClipboard('fermi (RRID:SCR_016652)', 'rrid:scr_016652')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016652" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016665/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016665">Centrifuge Classifier <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016665 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016665&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.ccb.jhu.edu/software/centrifuge/">http://www.ccb.jhu.edu/software/centrifuge/ <i class='fa fa-external-link'></i></a></p> <p>Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.</p> <p></p> <p> <strong>Proper citation:</strong> Centrifuge Classifier (RRID:SCR_016665) <a href="javascript:void(0)" onclick="copyTextToClipboard('Centrifuge Classifier (RRID:SCR_016665)', 'rrid:scr_016665')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016665" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_006442/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_006442">Bioconductor <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_006442 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_006442&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://www.bioconductor.org/">http://www.bioconductor.org/ <i class='fa fa-external-link'></i></a></p> <p>Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.</p> <p></p> <p> <strong>Proper citation:</strong> Bioconductor (RRID:SCR_006442) <a href="javascript:void(0)" onclick="copyTextToClipboard('Bioconductor (RRID:SCR_006442)', 'rrid:scr_006442')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_006442" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_015991/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_015991">Eagle <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_015991 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_015991&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://data.broadinstitute.org/alkesgroup/Eagle/">https://data.broadinstitute.org/alkesgroup/Eagle/ <i class='fa fa-external-link'></i></a></p> <p>Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.</p> <p></p> <p> <strong>Proper citation:</strong> Eagle (RRID:SCR_015991) <a href="javascript:void(0)" onclick="copyTextToClipboard('Eagle (RRID:SCR_015991)', 'rrid:scr_015991')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_015991" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_024758/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_024758">PEPATAC <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_024758 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_024758&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://pepatac.databio.org/en/latest/">https://pepatac.databio.org/en/latest/ <i class='fa fa-external-link'></i></a></p> <p>Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.</p> <p></p> <p> <strong>Proper citation:</strong> PEPATAC (RRID:SCR_024758) <a href="javascript:void(0)" onclick="copyTextToClipboard('PEPATAC (RRID:SCR_024758)', 'rrid:scr_024758')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_024758" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_006281/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_006281">Galaxy <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_006281 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_006281&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://galaxyproject.org/">http://galaxyproject.org/ <i class='fa fa-external-link'></i></a></p> <p>Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases.</p> <p></p> <p> <strong>Proper citation:</strong> Galaxy (RRID:SCR_006281) <a href="javascript:void(0)" onclick="copyTextToClipboard('Galaxy (RRID:SCR_006281)', 'rrid:scr_006281')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_006281" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_006793/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_006793">ENCODE <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_006793 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_006793&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://genome.ucsc.edu/ENCODE">http://genome.ucsc.edu/ENCODE <i class='fa fa-external-link'></i></a></p> <p>Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome.</p> <p></p> <p> <strong>Proper citation:</strong> ENCODE (RRID:SCR_006793) <a href="javascript:void(0)" onclick="copyTextToClipboard('ENCODE (RRID:SCR_006793)', 'rrid:scr_006793')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_006793" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_006873/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_006873">eXpress <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_006873 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 100+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_006873&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://bio.math.berkeley.edu/eXpress/index.html">http://bio.math.berkeley.edu/eXpress/index.html <i class='fa fa-external-link'></i></a></p> <p>THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.<br/>From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.<br/><br/>Software for streaming quantification for high-throughput DNA/RNA sequencing. <br/>Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.</p> <p></p> <p> <strong>Proper citation:</strong> eXpress (RRID:SCR_006873) <a href="javascript:void(0)" onclick="copyTextToClipboard('eXpress (RRID:SCR_006873)', 'rrid:scr_006873')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_006873" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016368/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016368">Bowtie 2 <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016368 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016368&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml">http://bowtie-bio.sourceforge.net/bowtie2/index.shtml <i class='fa fa-external-link'></i></a></p> <p>Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.</p> <p></p> <p> <strong>Proper citation:</strong> Bowtie 2 (RRID:SCR_016368) <a href="javascript:void(0)" onclick="copyTextToClipboard('Bowtie 2 (RRID:SCR_016368)', 'rrid:scr_016368')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016368" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016323/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016323">StringTie <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016323 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016323&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://ccb.jhu.edu/software/stringtie/">https://ccb.jhu.edu/software/stringtie/ <i class='fa fa-external-link'></i></a></p> <p>Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .</p> <p></p> <p> <strong>Proper citation:</strong> StringTie (RRID:SCR_016323) <a href="javascript:void(0)" onclick="copyTextToClipboard('StringTie (RRID:SCR_016323)', 'rrid:scr_016323')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016323" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_013291/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_013291">MACS <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_013291 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 1000+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_013291&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://github.com/macs3-project/MACS">https://github.com/macs3-project/MACS <i class='fa fa-external-link'></i></a></p> <p>Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.</p> <p></p> <p> <strong>Proper citation:</strong> MACS (RRID:SCR_013291) <a href="javascript:void(0)" onclick="copyTextToClipboard('MACS (RRID:SCR_013291)', 'rrid:scr_013291')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_013291" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016596/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016596">biobakery <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016596 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016596&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://bitbucket.org/biobakery/biobakery/wiki/Home">https://bitbucket.org/biobakery/biobakery/wiki/Home <i class='fa fa-external-link'></i></a></p> <p>Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis.</p> <p></p> <p> <strong>Proper citation:</strong> biobakery (RRID:SCR_016596) <a href="javascript:void(0)" onclick="copyTextToClipboard('biobakery (RRID:SCR_016596)', 'rrid:scr_016596')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016596" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016871/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016871">MARRVEL <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016871 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016871&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="http://marrvel.org/">http://marrvel.org/ <i class='fa fa-external-link'></i></a></p> <p>Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.</p> <p></p> <p> <strong>Proper citation:</strong> MARRVEL (RRID:SCR_016871) <a href="javascript:void(0)" onclick="copyTextToClipboard('MARRVEL (RRID:SCR_016871)', 'rrid:scr_016871')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016871" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="inner-results"> <div class="the-title"> <ul class="list-inline up-ul" style="margin:7px 0"> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> <i title="Log In to Use Collections" class="icon-sm fa fa-square-o btn-login" style="cursor:pointer"></i> </span> </li> <h3 style="display:inline-block; text-transform:none"> <div><a href="https://rrid.site/data/record/nlx_144509-1/SCR_016755/resolver?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20&i=rrid:scr_016755">Discovar assembler <i class="fa fa-file-o"></i></a></div> </h3> <li class="body-hide"> <style> .in-collection { color: green; } </style> <span class="coll-li"> </span> </li> <h4> RRID:SCR_016755 </h4> <span class="fa-stack fa-md"> <i class="fa fa-circle fa-stack-2x" style="color:#666767"></i> <i class="fa fa-line-chart fa-stack-1x fa-inverse"></i> </span> This resource has 10+ mentions. <a target="_self" href="/php/download-rin-rrid-mentions.php?viewid=nlx_144509-1&rrid=RRID:SCR_016755&tab=mentions&mode=all"><i class="fa fa-download" title="Download Mentions"></i></a> <span class="help-tooltip" data-name="mention-definition.html"></span>  </ul> </div>  <p><a target="_blank" href="https://software.broadinstitute.org/software/discovar/blog/">https://software.broadinstitute.org/software/discovar/blog/ <i class='fa fa-external-link'></i></a></p> <p>Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.</p> <p></p> <p> <strong>Proper citation:</strong> Discovar assembler (RRID:SCR_016755) <a href="javascript:void(0)" onclick="copyTextToClipboard('Discovar assembler (RRID:SCR_016755)', 'rrid:scr_016755')"> <i class="fa fa-clipboard"></i> Copy </a>   <span id="rrid:scr_016755" class="copy-alert" style="text-align: center; width:120px; display:none"></span> </p> <ul class="list-inline up-ul"> <li> <i class="fa fa-info"></i>   Source: <a href='https://rrid.site/rin/sources/SCR_005400' target='_blank'>SciCrunch Registry</a> </li> </ul> </div> <hr/> <div class="margin-bottom-30"></div> <div class="text-left"> <div class="text-left"><ul class="pagination"><li><a href="javascript:void(0)">芦</a></li><li class="active"><a class="not-rin" href="javascript:void(0)">1</a></li><li><a class="not-rin" href="https://rrid.site/data/source/nlx_144509-1/page/2/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20">2</a></li><li><a class="not-rin" href="https://rrid.site/data/source/nlx_144509-1/page/2/search?q=%2A&l=&facet[]=Keywords%3Aanalysis&facet[]=Funding%20Agency%3Anhgri%20&facet[]=Funding%20Agency%3Abergen%20research%20foundation%20">禄</a></li></ul></div> </div> <hr/> <div class="rin"> <div id="cant-find-rrid"> <div class="panel"> <div class="panel-body"> <p>Can't find your Tool?</p> <p>We recommend that you click <span class="btn btn-info help-tooltip-btn" data-name="rin-search-tips.html"><i class="fa fa-question-circle"></i></span> next to the search bar to check some helpful tips on searches and refine your search firstly. 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