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<html lang="en">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1">
<meta name="color-scheme" content="light">
<title>Transcriptomes Explorer</title>
<link rel="stylesheet" href="assets/style.css">
<script src="assets/plotly.min.js" defer></script>
<script src="assets/app.js" defer></script>
</head>
<body>
<main class="shell">
<header class="hero">
<h1>Transcriptomes Explorer</h1>
<p>Assembly, functional annotation, differential expression and enrichment analyses</p>
</header>
<nav class="tabs" aria-label="Explorer sections">
<button class="tab active" data-tab="overview">Overview</button>
<button class="tab" data-tab="expression">3D expression landscape</button>
<button class="tab" data-tab="de">Differential expression</button>
<button class="tab" data-tab="enrichment">Functional enrichment</button>
</nav>
<section id="overview" class="panel active">
<figure class="workflow-figure">
<img src="assets/transcriptome_workflow_space_v1.drawio.svg" alt="Integrated transcriptome workflow">
</figure>
<div class="table-wrap"><table id="assembly-table" class="data-table"></table></div>
<div class="controls">
<label>Select a species to explore the functional-annotation summary<select id="overview-species"></select></label>
</div>
<h2 id="annotation-title"></h2>
<div class="table-wrap"><table id="annotation-table" class="data-table"></table></div>
</section>
<section id="expression" class="panel">
<p class="caption">Sample-level expression is transformed as <code>log2(TMM + 1)</code>. Points are colored by development stage and shaped by temperature.</p>
<div class="controls">
<label>Species<select id="dim-species"></select></label>
<label>Reduction method<select id="dim-method"><option>PCA</option><option>UMAP</option></select></label>
<label>Most variable genes<select id="dim-genes"><option value="all">All expressed genes</option><option value="5000">5,000</option><option value="1000">1,000</option></select></label>
<button id="dim-run" class="primary">Compute 3D projection</button>
</div>
<div id="dim-plot" class="plot wide"></div>
<div id="dim-status" class="note">Choose settings and compute the projection.</div>
<div class="table-wrap"><table id="dim-table" class="data-table"></table></div>
</section>
<section id="de" class="panel">
<div class="controls">
<label>Species<select id="de-species"></select></label>
<label>Contrast<select id="de-contrast"></select></label>
<label>Method<select id="de-method"><option>DESeq2</option><option>edgeR</option></select></label>
<label>Maximum p-value<input id="de-pvalue" type="number" min="0" max="1" step="0.001" value="1"></label>
<label>Maximum adjusted p-value / FDR<input id="de-adjusted" type="number" min="0" max="1" step="0.001" value="0.05"></label>
<label>Minimum absolute fold change<input id="de-fold" type="number" min="0" step="0.1" value="0"></label>
<label>Volcano Y axis<select id="de-y"><option value="adjusted">Adjusted p-value / FDR</option><option value="pvalue">p-value</option></select></label>
<button id="de-run" class="primary">Query DEGs</button>
</div>
<div id="de-plot" class="plot wide"></div>
<div id="de-summary" class="note"></div>
<div class="table-wrap results-table-wrap"><table id="de-table" class="data-table"></table></div>
<button id="de-download" class="download">Download filtered differential-expression CSV</button>
</section>
<section id="enrichment" class="panel">
<div class="controls">
<label>Species<select id="en-species"></select></label>
<label>Contrast<select id="en-contrast"></select></label>
<label>Method<select id="en-method"><option>DESeq2</option><option>edgeR</option></select></label>
<label>Maximum p-value<input id="en-de-pvalue" type="number" min="0" max="1" step="0.001" value="1"></label>
<label>Maximum adjusted p-value / FDR<input id="en-de-adjusted" type="number" min="0" max="1" step="0.001" value="0.05"></label>
<label>Minimum absolute fold change<input id="en-de-fold" type="number" min="0" step="0.1" value="0"></label>
<label>Functional source<select id="en-source"></select></label>
<label>Hierarchy / level<select id="en-hierarchy"></select></label>
<label>Maximum ORA p-value<input id="en-pvalue" type="number" min="0" max="1" step="0.001" value="1"></label>
<label>Maximum ORA adjusted p-value<input id="en-adjusted" type="number" min="0" max="1" step="0.001" value="0.05"></label>
<button id="en-run" class="primary">Query ORA</button>
</div>
<div id="en-plot" class="plot wide"></div>
<div id="en-summary" class="note"></div>
<div class="table-wrap results-table-wrap"><table id="en-table" class="data-table"></table></div>
<button id="en-download" class="download">Download filtered enrichment CSV</button>
</section>
<footer>
<div id="inria-logo" class="institutional-footer"></div>
<p><a href="https://inria.cl/es" target="_blank" rel="noopener noreferrer">Inria Chile Research Center</a> and collaborators.</p>
</footer>
</main>
</body>
</html>
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