Reproduce iDEP analyses with auto-generated R Markdown

iDEP is a tool for interactive analysis of RNA-Seq data. After analyzing their data, users have the option to download a R Markdown file, toegether with other data files, to reproduce the entire workflow. This blog is both the easiest and the hardest of all. It is easy because everything below was automatically generated by iDEP; it is hard as I have to write code to write code when developing iDEP.

Blogdown notes

This website is created using RStudio following this tutorial with tips from Ming Tang. To start a new post, choose “New post” from Addins. Use Markdown for texts. Use RMarkdown if it contains R markdown to render plots, etc. Choose which files you want to work on from the right bottom window. Save the files changed and the webpage is rendered automatically in the Viewer window. To disable a widget, change the header from active=true to active=false

DESeq2 experimental design and interpretation

Update. 11/13/17 Thanks to Mike Love for pointing out an error. This is just my understanding. There maybe other errors. To allow complex study designs in iDEP(http://ge-lab.org/idep/), I tried to understand how factoral models are built and the desired results are extracted from DESeq2. The following is based on the help document from the resutls( ) function in DESeq2, plus some of Mike Love’s answers to questions from users.