Bioinformatics

Logistic regression and GTEx

Working with all sorts of data, it happens sometimes that we want to predict the value of a variable which is not numerical. For those cases, a logistic regression is appropriate. It is similar to a linear regression except that it deals with the fact that the dependent variable is categorical. Here is the formula for the linear regression, where we want to estimate the parameters beta (coefficients) that fit best our data : \begin{equation} Y_i = \beta_0 + \beta_1 X_i [...]

By | January 27, 2017|Categories: Bioinformatics, Data Analysis, Python|0 Comments

SNP Filtering with pyGeno

Looking over the contents of our growing blog (good job guys !), it occured to me that we had not yet posted an article pertaining to the fantastic (and homegrown !) bioinformatics resource that is pyGeno. It turns out I need to use pyGeno to generate data and it's also my turn to write a blog post, how convenient ! I'll focus the article on writing a SNP filter, which can be a bit surprising the first time you try [...]

By | December 9, 2016|Categories: Bioinformatics, Python|0 Comments

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

Bioinformatic in a container

A recent tendency coming from the world of cloud computing is gaining more and more popularity in the bioinformatic community. This tendency is to develop and deploy application in a container. This container contains not only the application but all the needed libraries and a minimalist version of the applications of the operating system. As soon as it is built, the container is ready for use on a host computer containing the environment required to start the container. For a [...]

By | July 21, 2016|Categories: Bioinformatics|0 Comments

Good resources to learn R

Since it's the summer vacations, why not take some time to learn R. There are numerous free resources online to dive into this powerful language. For whomever wants to learn it, the challenge more related to finding the time rather than finding resources. Videos Coursera is an inevitable for online learning. There are a few good video courses offered for R beginners that are more or less oriented toward genomics : https://www.coursera.org/learn/r-programming https://www.coursera.org/learn/exploratory-data-analysis https://www.coursera.org/learn/bioconductor (Bioconductor is a life science packages [...]

By | July 11, 2016|Categories: Bioinformatics, R|0 Comments