Chapter 9 Bookdown component

To enable better visualization and immediate delivery of the results, we employed a Bookdown output to present the key tables and figures after running the EA pipeline.

Bookdown is a book-like long-form report originated from R Markdown with dynamic graphics and user-friendly layouts. The bookdown document generated by our pipeline, an interactive webpage in HTML format, allows users to explore the results on a web browser without installing any specific software. It contains a high-level summary of the project, such as the data quality, significant covariates, as well as basic plots including PCA, heatmaps, and volcano plots. Further, it can be hosted in GitHub as exemplified here, for broad sharing especially in publication.

Here is a screenshot of a bookdown report generated after running the EA pipeline. It contains 5 sections showing multiple exploratory analysis figures: QC figures, Covariates, PCA, Volcano plots, and Heatmaps.