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Aizan's Secondary Blog

first foray into bioinformatics with R

Posted on 16 Mar 2018

Before we go straight into the content of this short write-up, here is a back story worth reading (I guess). When I was rotating back in fall semester 2017, I asked my then-PI (principal investigator, a.k.a research advisor) to suggest me a second rotation lab that was doing viral genomics. The response was “no, you should find yourself”.

Miraculously, perhaps unbeknownst to me, I got what I wanted. I enrolled into a class that I did not know would be a bit bioinformatics-heavy. At first all we did was trying not to be lost while navigating the UCSC Genome Browser, then the assignments metamorphed into trying our best to navigate the confusing R console / RStudio IDE (it is still confusing, but far less when I first started).

In hindsight, I am thankful. A brutal assignment on analyzing the transcription profile of 50k genes from 860 human samples (data from GTEx) by using R brought me to understand a number of things.

Here is a list of things to consider, as far as my experience is concerned.

List 01: DEA Analysis

List 02: R, RStudio, and Rmarkdown

This list is updated from time-to-time