Solution: use your ~/.my/cnfInside your ~/.my.cnf file define the connection parameters to your databases. For example, here I define two groups called local and toto:[local]user = rootpassword = ultra_secrethost = localhost[toto]user = capitaine_flamp...
A little improvement to the bigcor function proposed on Rmazing to compute huge correlation matrix in R, I made the function work in parallel using all the CPU cores available on the machine. The code is here.Here is a benchmark of the 2 func...
As air pollution in Beijing reach new high [NYT article]. I re-ran the analysis I put online a few months ago. "Crazy bad" is a good description when it reach those levels. But I am sure there are other place like Mexico city, LA etc... that also look...
The positive false discovery rate (pFDR) has become a classical procedure to test for false positive. It is one of my favourite because it rely on a re-sampling approach.I base my implementation on John Storey PNAS paper and the technical report he pub...
The Guardian DataBlog published yesterday an interesting article exploring graphically the religious intolerance across the world. The data are coming from a report published by Pew Research Center's Forum on Religion and Public Life. I like the philosophy DataBlog a lot, providing the raw data for everyone to look at. However, I felt that the visualization could be improved. First the data are longitudinal and no temporal representation is provided.…
One of the air pollution detection machine in Beijing (at the American Embassy) is connected to Twitter and tweet about the air quality in real time. By default the machine in Beijing output the 24hr summary PM2.5 air pollution information. What is PM2...
While speeding up some code the other day working on a project with a colleague I ended up trying Rcpp for the first time. I re-implemented the cosine distance function using RcppArmadillo relatively easily using bits and pieces of code I found scatter...
Our latest paper in PLoS Computational Biology is out.The project spanned over 2 years starting at the end of my first year of postdoctoral training until now. It has been a truly collaborative endeavor across institutions but also across sub-disciplin...
Building a network of interaction between a bunch of genes can help a great deal in understanding the relationships between the seemingly disparate elements from your list. It can seems challenging at first to build such network but it's less complicat...
Interpreting a list of differentially regulated genes can take many forms. One of the most widely used method is looking for enrichment of functional group of genes compared to a random sampling of gene from the same universe, namely an over-representa...
