MSEAp

An R package to perform Metabolite Set Enrichment Analysis (MSEA) for metabolomics community.

Running MSEAp on Binder

No installation needed. Please click badge. After that, you should see the Jupyter Notebook. In the Jupyter Notebook click on "New" > "RStudio Session". You should see RStudio next.

MSEAp is already installed in the RStudio environment. Please load MSEAp by running library(MSEAp) in the RStudio console.

Installation

# If you are using Debian or Ubuntu, please uncomment the next two lines
#system("sudo apt-get update")
#system("sudo apt-get install -y zlib1g-dev libxml2-dev libpng-dev")

install.packages(c("devtools", "webshot", "knitr", "rmarkdown"))

source("http://bioconductor.org/biocLite.R")
biocLite(c("KEGGREST", "KEGGgraph", "BiocStyle", "paxtoolsr", "RCy3"))

devtools::install_github("afukushima/MSEApdata", build_vignettes = FALSE)
devtools::install_github("afukushima/MSEAp", build_vignettes = TRUE)

Documents

browseVignettes("MSEAp")

Updates

version 0.0.9000 (Oct 17, 2017)

License

The MSEAp package is free software; a copy of the GNU General Public License, version 3, is available at http://www.r-project.org/Licenses/GPL-3