Incorporate dee2 data into your R-based RNA-seq workflow
Dee2.io is a portal for accessing gene expression data derived from public RNA-seq datasets. So far there are over 400k available datasets and its growing every day. While there are existing databases of such as Expression Atlas, Recount2 and ARCHS4, dee2.io offers a number of unique benefits. For instance, dee2 includes gene-wise counts fron STAR as well as transcript-wise quantifications from Kallisto. There are a few ways you can access these data. Firstly, there is a nice web interface that is mobile friendly. Secondly, there are data dumps available if you are running a large scale analysis. But the purpose of this post is to demonstrate the improved R interface in action together with SRAdbv2 and statistics with edgeR and DESeq. The official documentation is available on GitHub.
Getting started This tutorial provides a walkthrough for how to work with dee2 expression data, starting with dataset searches, obtaining the data from dee2.io and then performing a differential analysi…
Getting started This tutorial provides a walkthrough for how to work with dee2 expression data, starting with dataset searches, obtaining the data from dee2.io and then performing a differential analysi…