Project Description

Dr Momeneh (Sepideh) Foroutan

The University of Melbourne

Generating dynamic reports using R Markdown in RStudio

Getting started with bioinformatic software

Friday 5 July 2019

Dr Momeneh (Sepideh) Foroutan is a research fellow in computational cancer biology in the Department of Clinical Pathology of the University of Melbourne Centre for Cancer Research in the Victorian Comprehensive Cancer Centre.

Sepideh has Masters’ degree in Molecular Genetics from Shahid Beheshti University in Tehran, Iran. She moved to Melbourne in 2014 to pursue her PhD in computational cancer biology in the University of Melbourne’s Department of Surgery and the Bioinformatics Division of the Walter and Eliza Hall Institute of Medical Research. She is experienced in analysing transcriptomics data, large data integration, batch correction and data visualisation. She co-founded the R-Ladies Melbourne in 2016, as the first R-Ladies chapter in Australia, and is currently its main organiser.

Data analysts are routinely required to generate reports, which not only include results and conclusions from the analysis, but should also include details about data, methods, code or pipelines that were used to generate the results, as well as any necessary explanatory notes. Recording such details together with results ensures that methods are always linked, and helps ensure computational reproducibility.

In this talk, I introduce and demonstrate the use of R Markdown, which is an easy-to-write plain text format, and is designed to generate reports containing code chunks, figures and tables, as well as notes, all in one document. This avoids the labour of manual writing/maintaining reports and switching between different programs to generate reports.

R Markdown ensures the consistency and reproducibility of reports, and is easy to share between collaborators. These reports can be converted into different formats (e.g. html, PDF and Word), and may include static or interactive outputs.

Below is a link to Sepideh’s Github repository which includes the presentation (in RMD, HTML and PDF formats), as well as the dynamic report (in RMD and HTML formats) that she was presenting in her talk. The repo also includes the data that she used in that report.