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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Expression Data{%endblock%}
{%block pagetitle%}Expression Data{%endblock%}
{%block breadcrumb%}
<li class="breadcrumb-item">
<a href="{{url_for('base.index')}}">Home</a>
</li>
<li class="breadcrumb-item active">
<a href="{{url_for('expression-data.index.index')}}">Expression Data</a>
</li>
{%endblock%}
{%block contents%}
<div class="row">
{{flash_all_messages()}}
<h1 class="heading">data upload</h1>
<div class="explainer">
<p>Each of the sections below gives you a different option for data expression-data.
Please read the documentation for each section carefully to understand what
each section is about.</p>
</div>
</div>
<div class="row">
<h2 class="heading">R/qtl2 Bundles</h2>
<div class="explainer">
<p>This feature combines and extends the two upload methods below. Instead of
uploading one item at a time, the R/qtl2 bundle you upload can contain both
the genotypes data (samples/individuals/cases and their data) and the
expression data.</p>
<p>The R/qtl2 bundle, additionally, can contain extra metadata, that neither
of the methods below can handle.</p>
<a href="{{url_for('expression-data.rqtl2.select_species')}}"
title="Upload a zip bundle of R/qtl2 files">
<button class="btn btn-primary">upload R/qtl2 bundle</button></a>
</div>
</div>
<div class="row">
<h2 class="heading">Expression Data</h2>
<div class="explainer">
<p>This feature enables you to upload expression data. It expects the data to
be in <strong>tab-separated values (TSV)</strong> files. The data should be
a simple matrix of <em>phenotype × sample</em>, i.e. The first column is a
list of the <em>phenotypes</em> and the first row is a list of
<em>samples/cases</em>.</p>
<p>If you haven't done so please go to this page to learn the requirements for
file formats and helpful suggestions to enter your data in a fast and easy
way.</p>
<ol>
<li><strong>PLEASE REVIEW YOUR DATA.</strong>Make sure your data complies
with our system requirements. (
<a href="{{url_for('expression-data.index.data_review')}}#data-concerns"
title="Details for the data expectations.">Help</a>
)</li>
<li><strong>UPLOAD YOUR DATA FOR DATA VERIFICATION.</strong> We accept
<strong>.csv</strong>, <strong>.txt</strong> and <strong>.zip</strong>
files (<a href="{{url_for('expression-data.index.data_review')}}#file-types"
title="Details for the data expectations.">Help</a>)</li>
</ol>
</div>
<a href="{{url_for('expression-data.index.upload_file')}}"
title="Upload your expression data"
class="btn btn-primary">upload expression data</a>
</div>
<div class="row">
<h2 class="heading">samples/cases</h2>
<div class="explainer">
<p>For the expression data above, you need the samples/cases in your file to
already exist in the GeneNetwork database. If there are any samples that do
not already exist the upload of the expression data will fail.</p>
<p>This section gives you the opportunity to upload any missing samples</p>
</div>
<a href="{{url_for('expression-data.samples.select_species')}}"
title="Upload samples/cases/individuals for your data"
class="btn btn-primary">upload Samples/Cases</a>
</div>
{%endblock%}
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