Python

Dependency issue: In Conda, with SCENIC

I’ve been working with pySCENIC in the recent couples of months. It’s a tool that is meant to uncover gene sets that are controlled by transcription factors and suggests the underlying logic of how genes are regulated. It takes gene expression data from single-cell RNA sequencing and seems to be fairly easy to use. So, what took me several months? I did my preliminary run with their R implementaion, which was released earlier in the original reference.

psutil, python, and icc

I used to dislike dependency management because there are so many things that require root or are mysteriously incompatible with each other. However, I recently came to realize that the existence of dependency itself is a delicate and elegant system despite being messy at times. The recent occasion that reminded me the beauty of dependency was to install psutil on an HPC. It ran CentOS 7, and I had Python 3.