#60 Differential gene expression and DESeq2 with Michael Love

<p>In this episode, <a href="https://mikelove.github.io/">Michael Love</a> joins us to talk about the differential gene expression analysis from bulk RNA-Seq data.</p> <p>We talk about the history of Mike’s own differential expression package, <a href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html">DESeq2</a>, as well as other packages in this space, like <a href="https://bioconductor.org/packages/release/bioc/html/edgeR.html">edgeR</a> and <a href="https://bioconductor.org/packages/release/bioc/html/limma.html">limma</a>, and the theory they are based upon. Mike also shares his experience of being the author and maintainer of a popular bioninformatics package.</p> <p>Links:</p> <ul> <li><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2</a> (Love, M.I., Huber, W. &amp; Anders, S.)</li> <li><a href="https://bioconductor.org/packages/release/bioc/html/DESeq2.html">DESeq2 on Bioconductor</a></li> <li><a href="https://chanzuckerberg.com/eoss/proposals/ensuring-reproducible-transcriptomic-analysis-with-deseq2-and-tximeta/">Chan Zuckerberg Initiative: Ensuring Reproducible Transcriptomic Analysis with DESeq2 and tximeta</a></li> </ul> <p>And a more comprehensive set of links from Mike himself:</p> <blockquote> <p>limma, the original paper and limma-voom:<br /> <a href="https://pubmed.ncbi.nlm.nih.gov/16646809/">https://pubmed.ncbi.nlm.nih.gov/16646809/</a><br /> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053721/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053721/</a></p> </blockquote> <blockquote> <p>edgeR papers:<br /> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/</a><br /> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378882/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378882/</a></p> </blockquote> <blockquote> <p>The recent manuscript