Differential Expression and a Mild Rant
It's been a while since I posted anything here. I have been working on a stock trading bot on a proprietary platform so there hasn't been much that I can report in public. Over the last week, I have had a chance to take a look at some RNA-Seq data in order to look at differential expression in fly transposable elements (TE), also sometimes called repeat elements. There are a number of packages for RNA-Seq differential expression analysis. This Wikipedia article lists some of them. How do you decide which to use? I use the post-modern approach. There's no way to test all of them, so I Google for "RNA-Seq differential expression software" and get a list of candidates. Next, I ask colleagues what they use and look at the intersection of the two sets. From there, I just pick a couple of popular packages and try them out. Using this totally unscientific approach I settled on DESeq2 and edgeR . Both are well established Bioconductor packages for R . I tend to be an...