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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>GeNet | USER GUIDE</title>
<link rel="icon" href="img/logo/favicon.png" sizes="32x32" />
<link rel="icon" href="img/logo/favicon.png" sizes="192x192" />
<link rel="apple-touch-icon-precomposed" href="img/logo/favicon.png" />
<meta name="description" content="To walk you through each step in GeNet. This will guide you through the application by simply giving clear instructions">
<meta name="keywords" content="genet, gene expression, microarray">
<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Open+Sans|Candal|Alegreya+Sans">
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ul li{
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border : 2px solid #5FCF80;
}
</style>
<body>
<!--Navigation bar-->
<nav class="navbar navbar-default navbar-fixed-top">
<div class="container">
<div class="navbar-header">
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<img src="img/logo/logo.png" alt="logo" style="width:115px; margin-top: -3px;">
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<ul class="nav navbar-nav navbar-right">
<li><a href="index.php">Home</a></li>
<li><a style="color: #5fcf80;">User guide</a></li>
<li><a href="manual.php">Manual</a></li>
<li><a href="nomenclature.php">Nomenclature</a></li>
<li><a href="crash_courses.php">Crash course</a></li>
<li><a href="faq.php">Faq</a></li>
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<h2 class="text-dec">GeNet USER GUIDE</h2>
</div>
<div class="intro-para text-center quote">
<!-- <p class="big-text">From unrefined data to meaningful insights</p> -->
<p class="small-text">“To walk you through each step in GeNet. This will guide you through the application by simply giving clear instructions”</p>
</div>
</div>
</div>
</div>
</div>
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<hgroup>
<h3 class="det-txt-manual">Getting Started</h3>
<p class="det-p-manual">Are you a first time user? Then Sign up or sign in with your Google account. After that, you can just log in anytime you like.</p>
</hgroup>
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<hgroup>
<h3 class="det-txt-manual">Home Page</h3>
<p class="det-p-manual">Each component in the Home page corresponds to the specific tasks. You can initiate each step by clicking on the relevant steps. You cannot directly navigate to some steps without going through the previous steps. In any instance, the steps you can perform will be shown in a dark color mode. The steps you cannot yet perform will appear in a lighter color.</p>
</hgroup>
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<div class="detail-info">
<hgroup>
<h3 class="det-txt-manual">Tour around GeNet</h3>
<ul style="list-style-type: square; text-align: justify;">
<li>Click on the “START TOUR” to get simple tips and instructions.</li>
<li>Click on the bell icon at the bottom right corner of the page to mute/ unmute the tour.</li>
</ul>
</hgroup>
</div>
</div>
</div>
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<!--/ step_21-->
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<hgroup>
<h3 class="det-txt-manual">Upload Files</h3>
<ul style="list-style-type: square; text-align: justify;">
<li>If you want to upload a new data set, you can do so by clicking on the “Choose File”. You can choose the data set from your system. The file should be in comma-separated value (.csv) format.</li>
<li>If you just want to get hands-on experience with GeNet, you can just select a sample file by clicking on the “SELECT SAMPLE FILE” button.</li>
<li>You can view the sample file by downloading it through the “DOWNLOAD SAMPLE FILE” button.</li>
<li>After choosing your data set (.csv file) click on the “SUBMIT” button to continue.</li>
<li>Click on the “info” icon to get more information on the input format of the data file.</li>
</ul>
<h4 class="sm-txt-manual"><a href="manual.php#upload_link" target="_blank">Click here for more info on the input format</a></h4>
</hgroup>
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<hgroup>
<h3 class="det-txt-manual">Pre-processing</h3>
<ul style="list-style-type: square; text-align: justify;">
<li>Choose your data set by clicking on the drop-down menu in the “Available Files” tab. The drop-down will show you the list of already uploaded data sets.</li>
<li>Choose the corresponding annotation table by clicking on the drop-down menu of the “Annotation Table” tab.</li>
<li>Select any Probe Selection method from the drop-down menu of the Probe Selection method. You can choose 'other' option and upload a custom annotation table also.</li>
<li>If you want to proceed without mapping to gene symbols, click “SKIP MAPPING” button.</li>
<li>If you want to map the probe_IDs to gene symbols click “SUBMIT”.</li>
<li>If you want to get a quick glance at your data set, you can do so by clicking on the “View” button.</li>
<li><b>Interquartile Range:</b> You can choose the interquartile range of all the values corresponding to a particular gene symbol for each sample.</li>
</ul>
<h4 class="sm-txt-manual"><a href="manual.php#preprocess_link" target="_blank">Click here for more info on annotation tables and probe selection methods</a></h4>
</hgroup>
</div>
</div>
</div>
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<li>GeNet by default shows you 10 entries by page, you can change this number by changing the values at the “Show” icon.</li>
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<h4 class="sm-txt-manual"><a href="manual.php#view_tb_link" target="_blank">Click this to see more details on the data set</a></h4>
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<h4 class="sm-txt-manual"><a href="manual.php#imputation_link" target="_blank">Click here for more info on normalization and imputation.</a></h4>
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<h4 class="sm-txt-manual"><a href="manual.php#fold_link" target="_blank">Click this to get more info on Fold Change and P-Values</a></h4>
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<li>Input the number of genes that you like to proceed with. The tip is to get the number of genes corresponding to the knee point of the graph.</li>
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<h4 class="sm-txt-manual"><a href="manual.php#feature_reduction_link" target="_blank">Click this to get more info on this step</a></h4>
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<h4 class="sm-txt-manual"><a href="manual.php#feature_selection" target="_blank">Click here to learn more about feature selection methods</a></h4>
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<li>Click on each gene symbol to get more details on the functionality of the gene.</li>
<li>Click "MORE DETAILS" to view more details on the specific gene</li>
<li>View the list of genes by choosing either the “GRID” option or the “LIST” option.</li>
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<h4 class="sm-txt-manual"><a href="manual.php#results_link" target="_blank">Click here to understand the results better</a></h4>
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<h4 class="sm-txt-manual"><a href="manual.php#analysis_link" target="_blank">Click here to learn more about analysis steps</a></h4>
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<h4 class="sm-txt-manual"><a href="manual.php#analysis_results_link" target="_blank">Click here to learn more about this step</a></h4>
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<li>To compare your results with already available data, select the type of disease you want to check with.</li>
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<h4 class="sm-txt-manual"><a href="manual.php#final_results_link" target="_blank">Click here to get more information on the results obtained</a></h4>
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