R

R programming language

One task, three ways

Usually, there is more than one way to accomplish a task. Some are better, some are worse and others are just as good. Assessing which one to use is often related to the computing time, the ease of use and/or to personal preferences and abilities. Say I have a matrix of thousands of chromosomal features with the following column names : Feature, Start, End. All the positions are found on the same chromosome and the widths of my features are variable. [...]

By | 2017-05-01T10:25:02+00:00 January 15, 2015|Categories: Bioinformatics, R|0 Comments

Teach me how to box-plot!

Boxplots are everywhere! Publishers like boxplots.  But ask some people and most don't even know what a boxplot represents!  Recently I wanted to examine gene expression data between two samples for a certain gene. The gold standard to look at it would be *drum roll*... A boxplot! Interesting fact #1: Did you know a boxplot is called a “box and whiskers plot” as well?  Let's take a look! A boxplot is easily generated in the analysis software R and its interpretation [...]

By | 2017-04-29T15:41:25+00:00 September 21, 2014|Categories: Data Visualization, R, Statistics|0 Comments

RStudio and version control

A version control is just a way to keep track of changes made to files throughout time.  It allows you to return to previous versions later.  I bet you are already using one without even knowing it! When you copy a file or a script before modifying it, you're using version control.  However, your manual version control may become hard to deal with at some point.  That's why it's worth investing time early on in a project and use a [...]

By | 2017-05-01T10:21:46+00:00 June 10, 2014|Categories: R|Tags: , , |0 Comments

Rprofile

To be a good programmer/bioinformatician, you have to be a little bit lazy.   You need to get tired of doing tasks manually and know that putting some amounts of effort now will pay off later.  Laziness sometimes makes your more efficient and productive! For example, if you are tired of loading the same R packages manually everytime you open a new session or copy/pasting the required lines of code from script to script, there's a way to tell R to [...]

By | 2014-09-19T11:11:43+00:00 March 14, 2014|Categories: R|0 Comments

RStudio

When learning a new language (programming or other), it’s not always easy to get started.  10 years ago, I learned R using only the R console.  Today, RStudio is here to make our life easier.  I use this IDE everyday to write and execute R code!  This development environment built for R allows me to see at the same time my script, my console, graphs or help (the different panels can be customized).  The window where I write my script [...]

By | 2014-09-19T11:10:15+00:00 March 10, 2014|Categories: R|0 Comments