boucherg

About Geneviève

I’ve started in biochemistry but it is as a bioinformatician that I’ve been having fun for several years now : whether doing data analysis and visualization in R, building interactive web interfaces in javascript or exploring machine learning in python.

python and pandas

R is undeniably a must-use language. Especially for data visualization. But R can sometimes be a little bit slow when dealing with big datasets. If you don't need to create awesome graphs or don't have time to wait, there's an alternative in Python that can be quite fast for data manipulation. The Python Data Analysis Library, pandas, provides an easy way to manipulate data in python. Recently, I had to deal with a big gene expression file (21024 genes x [...]

By | 2017-04-29T15:49:18+00:00 April 17, 2014|Categories: Data Analysis, Python|Tags: , |1 Comment

What’s the fastest?

Often, we rely on our old habits. We get comfortable and have a tendency to do things the same old way. Same thing happens when you're programming. But a day will come when you’ll ask yourself, is this the fastest way to perform this task ? And when this happens to you (and if the given task is in Python), you’ll be glad that a package like timeit exist. Sure there are other ways to organize timing contest in Python. [...]

By | 2017-05-01T10:25:40+00:00 April 2, 2014|Categories: Performance, Python|0 Comments

lifelines (or doing survival analysis in Python)

Lately, I've been doing survival analysis.  I'm not an expert but we had a self-learning group based on David G. Kleinbaum and Mitchel Klein’s  book,   "Survival Analysis. A Self-Learning Text" .  At the end of this book, there's code provided to help you get started in SAS, Stata, SPSS and... R!  I've played with the R package survival which is quite good!  My problem was that I wanted to do survival analysis in Python.  I've started by doing it with [...]

By | 2017-04-29T17:16:41+00:00 March 24, 2014|Categories: Data Analysis, Python, Statistics|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