Preface

This thesis has been written using R Markdown with the bookdown package (Xie 2016, 2017). The renv package has been used to create a reproducible environment to build the thesis from source (Ushey 2019). All materials required to compile the thesis are available at https://github.com/sa-lee/thesis. An online version of the thesis is available to read at https://sa-lee.github.io/thesis.

Chapter 2 has been published in Genome Biology. It won the ACEMS Business Analytics Prize for Best Paper in 2019. Chapter 3 has been published in F1000 Research. Chapter 4 is based on my software contributions to the published article S. Lee et al. (2020). Chapter 5 has not been submitted.