resume/examples/Salomon/index.html

<h2 id="my-thesis">My thesis</h2>
<ul>
<li><a href="thesis-final.pdf">My thesis</a>: <em>Bioinformatic analysis of complex, high-throughput genomic and epigenomic data in the context of CD4⁺ T-cell differentiation and diagnosis and treatment of transplant rejection</em></li>
<li><a href="defense-slides.pdf">Slides for my defense talk</a>: The slides for my dissertation defense, mainly covering Chapter 2 of my thesis</li>
</ul>
<h2 id="interesting-sub-folders">Interesting sub-folders</h2>
<p>Each folder showcases a different project or aspect of my work in the Salomon lab.</p>
<ul>
<li><a href="Teaching"><code>Teaching</code></a>: Teaching materials for my lecture and lab on introductory RNA-seq analysis</li>
<li><a href="CD4"><code>CD4</code></a>: Examples relating to my CD4 memory RNA-seq &amp; ChIP-seq project</li>
<li><a href="450k"><code>450k</code></a>: Examples relating to analysis of Illumina 450k DNA methylation arrays</li>
<li><a href="Pathways"><code>Pathways</code></a>: Examples of gene set and pathway analysis for RNA-seq data</li>
<li><a href="globin"><code>globin</code></a>: Examples of my work in demonstrating the performance of a new globin blocking protocol for RNA-seq of blood tissues</li>
<li><a href="fRMA"><code>fRMA</code></a>: Examples and code from my work creating a custom frozen RMA reference to provide a stable normalization for machine learning applications</li>
</ul>
<h2 id="presentations">Presentations</h2>
<ul>
<li><a href="DGE%20Presentation.pdf"><code>DGE Presentation.pdf</code></a>: comparing edgeR, DESeq, and limma on both a conceptual and practical level</li>
<li><a href="Advanced%20RNA-seq%20Analysis.pdf"><code>Advanced RNA-seq Analysis.pdf</code></a>: On the advanced features provided by limma for RNA-seq analysis</li>
<li><a href="Reproducible%20Workflow%20Presentation.pdf"><code>Reproducible Workflow Presentation.pdf</code></a>: Showcases the use of <a href="https://snakemake.readthedocs.io/en/stable/">Snakemake</a> for building a reproducible analysis</li>
</ul>
<h2 id="other-files">Other files</h2>
<ul>
<li><a href="Classifier%20Math%20Write-up.pdf"><code>Classifier Math Write-up.pdf</code></a>: A short write-up to explain the mathematical principles behind the classifier method used in a machine learning project</li>
<li><a href="blockbuster-pipeline.R.html"><code>blockbuster-pipeline.R.html</code></a>: R code for clustering small RNA reads into clusters using <a href="http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html">Blockbuster</a></li>
<li><a href="mdsplots-multidim.pdf"><code>mdsplots-multidim.pdf</code></a>: A PCA plot of RNA-seq data for <em>C. elegans</em> samples with and without a drug that retards the aging process, demonstrating smaller age-related changes with the drug (for <a href="https://elifesciences.org/content/4/e08833">this paper</a>)</li>
</ul>