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<p>Website to share results of fucci-seq project.</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
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<li><a href="data-overview.html">Data description</a></li>
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<div id="combined-analysis" class="section level2">
<h2>Combined analysis</h2>
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<li><a href="combine-images-intensities.html">Make combined data</a></li>
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<div id="image-analysis" class="section level2">
<h2>Image analysis</h2>
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<li><p><a href="images-process.html">Processing images - from images to intensities</a></p></li>
<li>Image intensities
<ul>
<li><a href="confess-prelim.html">CONFESS results</a></li>
<li><a href="images-qc.html">QC analysis including no. nuclei detected, DAPI, and intensity variation</a></li>
<li><a href="images-qc-followup.html">Explore using log10 sum pixel intensity for signal metrics</a></li>
<li><a href="images-metrics.html">Compare correction approaches using median versus mean background</a></li>
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<li>Shape metrics
<ul>
<li><a href="images-metrics-cell-shape.html">Nucleus shape metrics versus intensities</a></li>
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<li>Normalize intensities by batch
<ul>
<li><a href="images-qc-labels.html">Visualize signal variation by plate and individual identity</a></li>
<li><a href="images-qc-variation.html">Visualize the structure of signal variation by individual identity</a></li>
<li><a href="images-normalize-quantile.html">Quantile normalization for GFP, RFP and DAPI</a></li>
</ul></li>
<li>Fitting cellcycleR
<ul>
<li><a href="images-cellcycleR.html">Parametric model across plates and individuals</a></li>
<li><a href="images-cellcycleR-convergence.html">Model convergence assessment</a></li>
</ul></li>
<li>Image inspection
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<li><a href="images-multiple-nuclei.html">Inspect images with multiple nuclei</a></li>
<li><a href="images-zero-nuclei.html">Inspect images with no nucleus</a></li>
</ul></li>
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<h2>QC</h2>
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<li><a href="sampleqc.html">Sample QC criteria</a><br />
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<li><a href="totals.html">Sequencing depth</a><br />
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<li><p><a href="reads-v-molecules.html">Reads versus molecules</a></p></li>
<li><p><a href="gene-filtering.html">gene filtering</a></p></li>
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