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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.

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 | 2017-04-29T16:57:17+00:00 July 11, 2016|Categories: Bioinformatics, R|Tags: |0 Comments

Machine learning in life science

Machine learning's popularity is increasing among bioinformaticians and biologists as it gives interesting results and has become more accessible than ever. A machine learning model can now be easily applied on a given dataset using R or Python packages. For example, the Python package Scikit-learn provides several algorithms (Random Forest, Support Vector Machine - SVM -, regression model and much more) and good documentation. Even deep machine learning (neural networks with multiple layers or convolutional networks for example) is more accessible [...]

By | 2016-11-08T09:30:05+00:00 May 18, 2016|Categories: Machine learning|0 Comments

What’s the fastest? – R edition

When I started using R, about ten years ago, the community was much smaller. No R-bloggers to get inspired or ggplot2 to make nice graphs. It was the beginning of an other implementation of R (other than CRAN's) known as Revolution R from Revolution Analytics. Their R targeted enterprise and was designed to be faster and more scalable. They also offer an open source version of their product called RRO. In April 2015, the company was acquired by Microsoft! May [...]

By | 2017-04-29T15:32:29+00:00 February 12, 2016|Categories: Performance, R|0 Comments

Permutations

Say we have the two following groups : g1 <- c(55, 65, 58) g2 <- c(12, 18, 32) We want to see if the two groups belong to the same distribution or can be considered as different groups. We might be tempted to try a Student’s t-test. t.test(g1, g2) ## Welch Two Sample t-test ## ## data: g1 and g2 ## t = 5.8366, df = 2.9412, p-value = 0.01059 ## alternative hypothesis: true difference in means is not equal [...]

By | 2017-04-30T10:15:37+00:00 October 14, 2015|Categories: Data Analysis, R, Statistics|0 Comments

Don’t ignore the warnings!

I'm sure that all of you R users have now noticed that sometimes R is talking to you. When you do something wrong, R replies with a message written in red in the console. How many of you actually read those error messages? If you take the time to read them carefully, you'll get a hint about what was wrong in your command. Let's look at an example: > sum(c('1','3','4','4')) Error in sum(c("1", "3", "4", "4")) : invalid 'type' (character) [...]

By | 2017-04-30T16:25:19+00:00 September 3, 2015|Categories: R, Statistics|0 Comments