performance optimization

Need for Speed — DESeq2

Making DESeq2 ready for Single Cell Data

Performance Debugging in R and C++

Two month ago, I started my PhD and the first assignment I got was to optimize the performance of an R package called DESeq2. In another blog post, I will describe in more detail about the success of that, but here I want to focus on the tools that helped me to navigate DESeq’s complex code base and identify the slow spots. For those not familiar with Bioinformatics and RNA-seq differential expression analysis, DESeq2 is one of the most popular tools for this task with more than 20,000 downloads each month.