PhD thesis

This repo contains source files for my PhD thesis, entitled

Fluent statistical computing interfaces for biological data analysis

Summary

This work contributes new computing interfaces for the analysis of data collected from technologies that measure changes in biology, like gene expression. The first interface is a new tool that unites data measured along the genome under a common language of transformation. This interface enables analysts to interpret and combine multiple results from different technologies in a clear and simple way. The second interface provides a framework for identifying interesting regions along the genome. The third interface empowers analysts to interrogate complex models using visual diagnostics. All are provided as open source software packages.

Reproducibility

The environment and R packages used to construct this thesis can be recovered using the renv package. Run the following code to install the packages used in this thesis:

# install.packages("renv")
renv::restore()

The thesis can be compiled into both html and pdf format as follows:

# uncomment if cache isn't setup
# make hub
# make bfcbam
# make bfcsnp
make both

Caching local resources

The data-raw/ directory provides scripts used to download and cache large/raw files contained in this thesis. These are then managed and transferred into R friendly data formats and managed with BiocFileCache and AnnotationHub.

Processed data files are stored as .rds and are located in the data directory.

These files can be created via BiocFileCache by running the following at the command line:

make hub
make bfcbam
make bfcsnp

Project Structure

Rmd/: R Markdown source documents for thesis document.
scripts/: R code to reproduce tables, figures and analyses for each chapter.
renv/: Package environment captured by renv
data/: Cleaned data used for thesis document.
data-raw/: R code to generate data in data/..
img/: Images made with other tools to illustrate ideas.
video/: Videos made with other tools to illustrate ideas. These are in mp4 format, screenshots are provided in the pdf version.
bib/: Bibliography files.
template/: Monash thesis template from robjhydman/MonashThesis.
docs/: the compiled thesis as pdf and website.

Acknowledgements