Biology

Introduction to cowplot to combine several plots in one with R

Hi everyone, Today I will introduce cowplot, an extension of ggplot2 library. Some helpful extensions and modifications to the 'ggplot2' package. In particular, this package makes it easy to combine multiple 'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. As you can see, this library can be useful to easily create a figure containing multiple plots. But we will see how we can use it to create [...]

By | November 28, 2016|Categories: Bioinformatics, Biology, Data Analysis, Data Visualisation, R|0 Comments

Draw me a Circos

How pretty would that look in my article? Very Pretty! As well as being informative! You might want to use a Circos for your own personal analysis or as an article figure. In both cases, this kind of representation is useful when it comes to visualizing data in a more global or complete manner:  you can have multiple types of data ranging across various chromosomal sequences. However, as wonderful and exciting the idea of having your own personal Circos might [...]

By | August 20, 2015|Categories: Bioinformatics, Biology, Data Visualisation|0 Comments

Table-reading: loading data into R without a hassle

The first thing I have learned in R is how to load a table. Usually, when you start your R journey, someone more knowledgeable will tell you how to do this very first action. It will typically be: data<-read.table("~/SomeFolder/datafile.txt") You probably will be adding various parameters into the brackets such as "row.names=0" or "header=TRUE" or, "sep="\t"", to make sure you are reading your file correctly. And this is perfectly fine, as a loading method of small datasets. However, to maximize [...]

By | February 5, 2015|Categories: Bioinformatics, Biology, Performance, R|1 Comment

Tweaking Fisher’s exact test for biology

Fisher's exact test is widely applied in bioinformatics (it is the core computation in gene-set or pathway enrichment analysis).  I won't introduce the test itself as others have done it several times (here), but will rather point to a disconnect between what it does and what is often needed. In Fisher's exact test, the null hypothesis is that there is no enrichment between the two variables studied.  When using this test with large numbers (such as the number of genes [...]

By | December 8, 2014|Categories: Bioinformatics, Biology, Statistics|Tags: |0 Comments

Gene symbols : the challenge

Almost certainly, one day, you'll have between your hands a list of outdated gene symbols. And you'll probably think that updating them is a straightforward task, but it's not that simple! Because there's the word 'bio' in bioinformatician, updating the gene symbols reminds me of the futile cycle. According to Wikipedia's definition, a futile cycle occurs when two metabolic pathways run simultaneously in opposite directions and have no overall effect other than to dissipate energy in the form of heat**.  Updating the [...]

By | September 29, 2014|Categories: Bioinformatics, Biology|0 Comments