Data Science

Tips for publishing your first document with bookdown and RStudio

I have just published my first document with bookdown and I am feeling euphoric at the moment. Somehow this gives me a very different satisfaction as compared to creating just a google document. Yes, they serve almost the same function, but the presentation of a bookdown document is much better. It also provides more functionalities and flexibilities than a google doc. Here are the minimal steps needed to customize a document from Yihui’s guide.

Utilisation of bioinformatics data

I am writing this post not as a guideline, but mainly for self-reference and hopefully a prompt for discussion. The boom of bioinformatics in recent years is coupled with cheaper technologies and consequently the surge of the amount of data available. The rapid development of the field itself is an anti-estblishment movement - even the most experienced bioinformaticians must spend a significant amount of time getting updated with the resources and toolkits.

Working with multi-thread machine

Compreesion tar cf - paths-to-archive | pigz -9 -p 32 > archive.tar.gz

A R package that creates blank Rmd files

I have created this package to create a blank Rmd file by saving a nearly blank Rmd template to the menu when you create Rmd files. I think it at least follows the first half of the UNIX orthodox: programs that do one thing and do it well. 😂 Reflection: the main purpose for me to create this package, other than making life easier, is to practise how to publish a R package onto github and to install it from there.

How to plot a bar plot with bars and labels between tick marks

I had this quesition when preparing my manuscript and a quick search brings me to this stackoverflow question by Johanna. I find the answer by Henrick to be highly effective, but can be further elaborated so that readers can be clearer about the functions of each line. Thus, I will base my post largely on Henrick’s answer but at the same time add my explanation to the rationale behind the lines.