README.md

In afukushima/MSEApdata: Metabolite-set data collection for pathway analysis in metabolomics

MSEApdata

The MSEApdata package is the companion to MSEAp. This package includes metabolite-set data collections that are utilized for the Metabolite Set Enrichment Analyses (MSEA) method for large-scale metabolite profiles. It includes Ecoli, Human and Mouse, and plants of the MetaCyc database (Caspi et al. NAR 44:D471-D480, 2016) and SMPDB (Jewison et al. NAR 42: D478-D484, 2014). It contains the following, which are necessary for metabolite-set enrichment analysis with MSEAp:

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

Documents

browseVignettes("MSEApdata")

Metabolite-set data

MSEApdata::supported.msets() lists all available metabolite-sets for MSEAp.

MSEApdata::supported.msets()

Example data for MSEAp

We included mset_AraCyc_format_KEGG and mset_PlantCyc_format_KEGG, both for plant metabolomics study.

afukushima/MSEApdata documentation built on May 3, 2019, 11:52 p.m.