The vespa R-packages requires installation of several dependencies, including the vespa.db R-package. In addition, it requires roxygen2, devtools and pkghelper to be installed to generate all necessary files for building the documentation.
Within R execute the following commands:
# install dependencies from CRAN
install.packages(c('devtools','data.table','pbapply','seqinr','stringr','mixtools','plyr','reshape2','tidyr','BiocManager','caret') ,dependencies=TRUE, repos='http://cran.rstudio.com/')
# install dependencies from BioConductor
BiocManager::install(c('viper','preprocessCore','limma'))
# install vespa
library(devtools)
install_github("califano-lab/vespa.db")
install_github("califano-lab/vespa")
For further information on usage, refer to the vespa.tutorial documentation, as well as the R-package help pages for information on individual functions:
library(vespa)
help(package="vespa")