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<h1 class="title toc-ignore">Home</h1>
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<p>Website to share results of fucci-seq project.</p>
<div id="overview" class="section level2">
<h2>Overview</h2>
<ul>
<li><a href="data-overview.html">Data description</a></li>
</ul>
<hr />
<p>..</p>
</div>
<div id="microscopy-image-analysis" class="section level2">
<h2>Microscopy image analysis</h2>
<ul>
<li><p><a href="images-process.html">Processing images - from images to intensities</a></p></li>
<li>Image inspection
<ul>
<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>
<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>
</ul></li>
<li>Shape metrics
<ul>
<li><a href="images-metrics-cell-shape.html">Nucleus shape metrics versus intensities</a></li>
</ul></li>
<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>transgene count in sequencing data
<ul>
<li><a href="images-transgene.html">Investigate zero-count transgenes</a></li>
</ul></li>
<li>Evalute categorical labeling
<ul>
<li><a href="images-pam.html">Cluster samples by Partition around medoids(PAM)</a></li>
<li><a href="images-mclust.html">Cluster samples by Mixture modeling</a></li>
<li><a href="images-subset-silhouette.html">Select a subset using silhouette index</a></li>
<li><a href="images-classify-fucci.html">Expression profiles of the “best” samples</a></li>
<li><a href="images-classify-leng.html">Expression profiles of sorted cells in Leng et al. 2015</a></li>
</ul></li>
</ul>
<hr />
</div>
<div id="rna-seq-data" class="section level2">
<h2>RNA-seq data</h2>
<ul>
<li></li>
</ul>
<hr />
</div>
<div id="model-fitting" class="section level2">
<h2>Model fitting</h2>
<ul>
<li>Evaluating cellcycleR 0.1.6
<ul>
<li><a href="images-cellcycleR-convergence.html">Model convergence assessment</a></li>
<li><a href="images-cellcycleR.html">Fitting on intensities across plates and individuals</a></li>
<li><a href="cellcycler-seqdata.html">Fitting on sequencing data that have independent cell cycle measurements (both Leng and Fucci)</a></li>
</ul></li>
</ul>
<hr />
</div>
<div id="qualty-control" class="section level2">
<h2>Qualty Control</h2>
<ul>
<li>Sample QC and filtering
<ul>
<li><a href="sampleqc.html">Sample QC criteria</a><br />
</li>
<li><a href="totals.html">Sequencing depth</a><br />
</li>
<li><a href="reads-v-molecules.html">Reads versus molecules</a></li>
</ul></li>
<li>Gene QC and filtering
<ul>
<li><a href="gene-filtering.html">gene filtering</a></li>
<li><a href="pca-tf.html">PCA with technical fators</a></li>
</ul></li>
</ul>
<hr />
</div>
<div id="one-time-investigations" class="section level2">
<h2>One-time investigations</h2>
<ul>
<li><a href="ensembl.html">Why some gene symbols (genes) correspond to multiple Ensembl IDs?</a></li>
</ul>
</div>
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