Differential expression analysis R code for FADS experisment

Version 1

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. The Digital Salmon will be an ensemble of mathematical descriptions of salmon physiology, combining mathematics, high-dimensional data analysis, computer science and measurement technology with genomics and experimental biology into a concerted ...

Towards the Digital Salmon: From a reactive to a pre-emptive research strategy in aquaculture (DigiSal)

Salmon farming in the future must navigate conflicting and shifting demands of sustainability, shifting feed prices, disease, and product quality. The industry needs to develop a flexible, integrated basis of knowledge for rapid response to new challenges. Project DigiSal will lay the foundations for a Digital Salmon: an ensemble of mathematical descriptions of salmon physiology, combining ...

The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.

Differential expression analysis (using R package edgeR) on liver gene expression between salmon with all four fads2 genes knockout, only fads2d6b & fads2d6c knockout and wildtype. All salmon was given either a low-PUFA diet or a high-PUFA diet