New version of the bitools docker container

Posted Leave a commentPosted in Docker

I updated the docker container that I maintain (bitools) to keep all the bioinformatics tools together that I recently use. Yesterday I added the tool FEELnc to it, a tool to detect lncRNAs from RNA-seq data.

UPDATE: Apparently there was an issue with the Forkmanages perl module in the docker container, I fixed that on 7.12.2017 and udated the docker image v0.1.6 on Docker Hub.

New publication

Posted Leave a commentPosted in Publication

The November issue of Computer Methods and Programs in Biomedicine
contains an article about my R-package ‘GenomicTools’:

http://www.sciencedirect.com/science/article/pii/S0169260716308549

The R-package GenomicTools for multifactor dimensionality reduction and the analysis of (exploratory) Quantitative Trait Loci

Background and objectives

We introduce the R-package GenomicTools to perform, among others, a Multifactor Dimensionality Reduction (MDR) for the identification of SNP-SNP interactions. The package further provides a new class of tests for an (exploratory) Quantitative Trait Loci analysis that overcomes some of the limitations of other popular (e)QTL approaches. Popular (e)QTL approaches that use linear models or ANOVA are often based on over-simplified models that have weak statistical properties and which are not robust against outlying observations.

Method

The algorithm to calculate the MDR is well established. To speed up its calculation in R, we implemented it in C++. Further, our implementation also supports the combination of several MDR results to an MDR ensemble classifier. The (e)QTL test procedure is based on a generalized Mann-Whitney test that is tailored for directional alternatives, as they are present in an (e)QTL analysis.

Results

Our package GenomicTools provides functions to determine SNP combinations that have the highest accuracy for a MDR classification problem. It also provides functions to combine the best MDR results to a joined ensemble classifier for improved classification results. Further, the (e)QTL analysis is based on a solid statistical theory. In addition, informative visualizations of the results are provided.

Conclusion

The here presented new class of tests and methods have an easy to apply syntax, so that also researchers inexperienced in R are able to apply our proposed methods and implementations. The package creates publication ready Figures and hence could be a valuable tool for genomic data analysis.

Exactly my type of humor

Posted Leave a commentPosted in News

In Germany abortions are illegal, but are not prosecuted, if they are performed within the first 12 pregnancy weeks and after the woman went to two(?!) consulting meetings. One thing that is, however, prosecuted is when a doctor advertises his or her service for abortion, especially if they have any financial interest or such. 

There was now a doctor in Germany who wrote on her webpage, that she performs abortions amd for an initiative called ‘Nie wieder!’ that was enough to suit her for violation of that paragraph 219a. The reason for doing so is, that the doctor shouldn’t advertise her service. The story becomes funny, when one notices that the head of that ‘Nie Wieder!’ association runs a webpage called www.abtreiber.com , where he lists some kind of ‘list of shame’ of doctors in Germany who perform or did perform abortions. In other words, they have a much more complete list of people whom to contact for an abortion than anybody else and they even do that PUBLIC!

So what do those guys want?! They suit individuals for advertising a service (that should be removed in their opinion), but offer at the same time a complete list of people who also offer that service. Seriously, what is the rational behind some peoples doing?!

Source: https://www.taz.de/Archiv-Suche/!5444891/

It has been a while

Posted Leave a commentPosted in Life

Today I realized, it has been a while that I added any content to this page, my apologies for that. It has been some kind of a summer… Lot of things happened, that kept me from writing things here, but I hope now things are getting more regular again.

I started today to improve the Recipe section on the page, I think it will be now much more convenient to navigate through the different recipes, I also continued to add more recipes to the page.