Install using devtools
devtools::install_github("Meshinchi-Lab/DeGSEA")
The package was developed for use in the Meshinchi lab to help streamline the association of clinical covariates and RNA-seq expression data. The clincal data elements are can be found at the TARGET data matrix. The RNA-sequencing data can be found at the Genomic Data Commons under project ID "TARGET-AML".
Its aim is only to simplify the workflows of differential expression analysis, GSEA, and unsupervised clustering methods, as well the data vizualization using open source, publicly avaialble R packages such as limma and edgeR.
Note that some functions are fairly outdated, but are retained for backwards compatibility of analyses run from ~2017 - 2018.
Author: Jenny Leopoldina Smith
ORCID: 0000-0003-0402-2779