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September 7, 2021

History of DESeq2, biostats with Frank Harrell and the surprises of infinity

1 - History of DESeq2 and more

In this podcast, Michael Love talks about the development and concepts behind DESeq2. Moreover, the podcast gives us a glimpse of what it takes for developing and mantaining a very famous method and bioconductor package.

https://bioinformatics.chat/deseq2

2 - RStudio Server and docker: making science more reproducible

Docker is an amazing tool that makes science more reproducible. Also, RStudio Server makes it easy to analyse data wherever you are if you have a workstation. In the blog post below, the author nicely explains how to set up RStudio Server within a docker image.

https://davetang.org/muse/2021/04/24/running-rstudio-server-with-docker/

3 - Clinical trial design and bayesian inference

Another podcast, another researcher. Frank Harrell, a biostatistician at Vanderbilt University working on clinical trial designs, explains how he went from the frequentist to the bayesian paradigm in statistics and how this has reflected in his work.

https://www.learnbayesstats.com/episode/45-biostats-clinical-trial-design-frank-harrell

4 - scRNA-seq, differential expression analysis and causal inference

Single-cell RNA sequencing has been rapidly growing. Methods to analyse such data are constantly being developed. In the following paper, authors introduce a causal framework to do differential expression analysis of scRNA-seq data.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02438-4

5 - Banach-Tarski theorem and the surprises of infinity

Infinity is a tricky concept in mathematics. Unintuitive results show up all the time due to this. Max Levy writes for Quanta Magazine about the Banach-Tarski theorem, which states you can split an orange in two identical copies of the original. Counter intuitive and amazing!

https://www.quantamagazine.org/how-a-mathematical-paradox-allows-infinite-cloning-20210826/

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