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.
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.
Recently, I analyzed a few single cell RNA-seq datasets and experimented with several new tools from recent publication. While it was fun, most datasets were just too large for my poor laptop to process, and I relied a lot on our server.