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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>refine.bio examples</title>
<link rel="preconnect" href="https://fonts.gstatic.com">
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// bootstrap
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css" integrity="sha384-HSMxcRTRxnN+Bdg0JdbxYKrThecOKuH5zCYotlSAcp1+c8xmyTe9GYg1l9a69psu" crossorigin="anonymous">
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<link href="index.css" rel="stylesheet" />
// viewport rules
<meta name="viewport" content="width=device-width, initial-scale=1">
</head>
<body>
<!-- NAVIGATION -->
<!-- Navigation header for refine.bio example Rmarkdown notebooks -->
<nav class="navbar navbar-default navbar-fixed-top">
<div class="container-fluid container-nav">
<div class="navbar-inverse">
<!-- NOTE: add "navbar-inverse" class for an alternate navbar background -->
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="">
<img src="components/refine-bio-ex-logo.svg" alt="refine.bio examples">
</a>
<div id="navbar" class="navbar-collapse collapse">
<!-- This outer list is the main navigation menu elements -->
<ul class="nav navbar-nav">
<!-- Getting started (no dropdown) -->
<li><a href="01-getting-started/getting-started.html">Getting Started</a></li>
<!-- Microarray Dropdown -->
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Microarray<span class="caret"></span></a>
<ul class="dropdown-menu">
<!-- Individual microarray pages go in this list -->
<li><a href="02-microarray/00-intro-to-microarray.html">Introduction</a></li>
<li><a href="02-microarray/clustering_microarray_01_heatmap.html">Clustering and Heatmaps</a></li>
<li><a href="02-microarray/differential-expression_microarray_01_2-groups.html">Differential Expression - 2 groups</a></li>
<li><a href="02-microarray/differential-expression_microarray_02_several-groups.html">Differential Expression - Several groups</a></li>
<li><a href="02-microarray/dimension-reduction_microarray_01_pca.html">Dimension Reduction - PCA</a></li>
<li><a href="02-microarray/dimension-reduction_microarray_02_umap.html">Dimension Reduction - UMAP</a></li>
<li><a href="02-microarray/pathway-analysis_microarray_01_ora.html">Pathway Analysis - ORA</a></li>
<li><a href="02-microarray/pathway-analysis_microarray_02_gsea.html">Pathway Analysis - GSEA</a></li>
<li><a href="02-microarray/pathway-analysis_microarray_03_gsva.html">Pathway Analysis - GSVA</a></li>
<li><a href="02-microarray/gene-id-annotation_microarray_01_ensembl.html">Ensembl Gene ID Annotation</a></li>
<li><a href="02-microarray/ortholog-mapping_microarray_01_ensembl.html">Ortholog Mapping</a></li>
</ul>
</li> <!--/microarray dropdown-->
<!-- RNA-Seq dropdown -->
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">RNA-seq<span class="caret"></span></a>
<ul class="dropdown-menu">
<!-- Individual RNA-Seq pages go in this list -->
<li><a href="03-rnaseq/00-intro-to-rnaseq.html">Introduction</a></li>
<li><a href="03-rnaseq/clustering_rnaseq_01_heatmap.html">Clustering and Heatmaps</a></li>
<li><a href="03-rnaseq/differential-expression_rnaseq_01.html">Differential Expression</a></li>
<li><a href="03-rnaseq/dimension-reduction_rnaseq_01_pca.html">Dimension Reduction - PCA</a></li>
<li><a href="03-rnaseq/dimension-reduction_rnaseq_02_umap.html">Dimension Reduction - UMAP</a></li>
<li><a href="03-rnaseq/gene-id-annotation_rnaseq_01_ensembl.html">Ensembl Gene ID Annotation</a></li>
<li><a href="03-rnaseq/ortholog-mapping_rnaseq_01_ensembl.html">Ortholog Mapping</a></li>
<li><a href="03-rnaseq/pathway-analysis_rnaseq_01_ora.html">Pathway Analysis - ORA</a></li>
<li><a href="03-rnaseq/pathway-analysis_rnaseq_02_gsea.html">Pathway Analysis - GSEA</a></li>
<li><a href="03-rnaseq/pathway-analysis_rnaseq_03_gsva.html">Pathway Analysis - GSVA</a></li>
</ul>
</li><!--/rna-seq dropdown-->
<!-- Advanced topics dropdown -->
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Advanced Topics<span class="caret"></span></a>
<ul class="dropdown-menu">
<!-- Individual Advanced topics pages go in this list -->
<li><a href="04-advanced-topics/00-intro-to-advanced-topics.html">Introduction</a></li>
<li><a href="04-advanced-topics/network-analysis_rnaseq_01_wgcna.html">Network Analysis - WGCNA</a></li>
</ul>
</li><!--/advanced dropdown-->
</ul>
<!-- Right side menubar -->
<ul class="nav navbar-nav navbar-right hidden-sm">
<li><a href="https://www.refine.bio"> Back to refine.bio</a></li>
<li><a href="https://share.hsforms.com/1pQ8pPB70TuG37sVjr-KtXA336z0">Give Feedback</a></li>
</ul>
</div>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</nav><!--/.navbar -->
<main>
<div id="hero">
<div class="wrapper">
<div class="flex flex-medium">
<p>
Explore a variety of example analyses like clustering, differential expression, pathway analysis, etc., for refine.bio datasets.
</p>
<img src="components/images/hero-image.png">
</div>
</div>
</div>
<div id="how-to">
<div class="wrapper">
<div class="flex flex-column">
<p>
How to use these examples
</p>
<p class="text">
These examples are available as R notebooks (.Rmd) and can be modified for your refine.bio dataset.
</p>
</div>
</div>
<div class="wrapper">
<div class="flex flex-large flex-top">
<div>
<p>
Set up
</p>
<p class="text">
The examples are written in R and use a variety of libraries. Get started by installing the required tools and libraries.
</p>
</div>
<div>
<p>
Download and follow along an example analyses
</p>
<p class="text">
You can use the refine.bio dataset that we use in analysis or you can use a different refine.bio dataset, relevant to your research interests.
</p>
</div>
</div>
</div>
</div>
<div id="examples">
<div class="examples">
<div class="wrapper">
<p>RNA-seq Examples</p>
</div>
<div class="wrapper">
<div class="flex flex-small">
<a href="03-rnaseq/clustering_rnaseq_01_heatmap.html" style="background-image: url(components/images/heatmap_SRP070849_annotated.png)">
<p>Clustering and Heatmaps</p>
</a>
<a href="03-rnaseq/differential-expression_rnaseq_01.html" style="background-image: url(components/images/SRP123625_volcano_plot.png)">
<p>Differential Expression</p>
</a>
<a href="03-rnaseq/dimension-reduction_rnaseq_01_pca.html" style="background-image: url(components/images/SRP133573_pca_plot.png)">
<p>Dimension Reduction - PCA</p>
</a>
<a href="03-rnaseq/pathway-analysis_rnaseq_02_gsea.html" style="background-image: url(components/images/SRP123625_gsea_enrich_negative_plot.png)">
<p>Pathway Analysis - GSEA</p>
</a>
</div>
</div>
</div>
<div class="examples">
<div class="wrapper">
<p>Microarray Examples</p>
</div>
<div class="wrapper">
<div class="flex flex-small">
<a href="02-microarray/clustering_microarray_01_heatmap.html" style="background-image: url(components/images/GSE24862_heatmap_annotated.png)">
<p>Clustering and Heatmaps</p>
</a>
<a href="02-microarray/differential-expression_microarray_01_2-groups.html" style="background-image: url(components/images/GSE71270_volcano_plot.png)">
<p>Differential Expression</p>
</a>
<a href="02-microarray/dimension-reduction_microarray_01_pca.html" style="background-image: url(components/images/GSE37382_pca_scatterplot.png)">
<p>Dimension reduction - PCA</p>
</a>
<a href="02-microarray/pathway-analysis_microarray_02_gsea.html" style="background-image: url(components/images/GSE71270_gsea_enrich_positive_plot.png)">
<p>Pathways Analysis- GSEA</p>
</a>
</div>
</div>
</div>
</div>
</main>
<!-- FOOTER -->
<div id="footer" class="navbar navbar-default navbar-footer">
<div class="container-fluid">
<div class="container">
<div class="col-md-6">
<p class="footer-text">
refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the
<a href="https://www.ccdatalab.org/" target="_blank" rel="noopener noreferrer">Childhood Cancer Data Lab (CCDL)</a>
</p>
</div>
<div class="col-md-6">
<ul class="nav navbar-nav">
<li>
<a href="https://share.hsforms.com/1pQ8pPB70TuG37sVjr-KtXA336z0" class="button">Give us feedback</a>
</li>
<li>
<a href="https://github.com/AlexsLemonade/refinebio-examples" class="button">GitHub</a>
</li>
<li>
<a href="https://www.refine.bio" class="button">refine.bio</a>
</li>
</ul>
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