The sev package is a utility package that relies completely on the bioconductor packages DEP and iSEE / iSEEu for the analysis, adding convenience functions, imputation methods, GO-term enrichment via clusterProfiler and additional iSEE containers.
Open up R and run the following code:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
if (!require("devtools", quietly = TRUE))
install.packages("devtools")
if (!require("DO.db", quietly = TRUE))
install.packages("DO.db")
#All other dependencies are installed automatically with sev.
devtools::install_github("adhutz/sev")
An examplary analysis is included as a vignette.
vignette("sev")
The examplary analysis is also included in the installation folder as an Rmarkdown document together with the proteinGroups.txt file. To open the corresponding folder directly, run the following code.
utils::browseURL(system.file("extdata", package = "sev"))