fgcz.gsea.ora

An R package for running enrichment analysis.

A plethora of R packages exist on CRAN and Bioconductor to perform over-representation analysis (ORA) and gene set enrichment analysis (GSEA). However, consistency in the underlying nomenclature for specific analyses and user friendly implementation is still lacking. fgcz.gsea.ora aims at unifying ID mapping and enrichment analysis in a syntactically coherent and intuitive way, while ensuring reproducibility of results.

fgcz.gsea.ora primarily consists of wrapper functions around the r CRANpkg("sigora") and r CRANpkg("WebGestaltR") packages from CRAN and r CRANpkg("rmarkdown") based reports for visualisation and contextualisation of analysis results.

1. Future plans

1. Integration of the R packages r Biocpkg(topGo) and r CRANpkg("enrichr")
2. Providing executable R script files, which can be run on windows or linux.

2. System requirements

2.1 Currently the software have been tested on the following systems

platform	platform version	R version
Windows	10 x64	R-3.6.2

3. Installation guide:

3.1 Dependancies

Run the following lines in R to make sure all required ackages are installed

list_of_packages <- c("AnnotationDbi", "BiocStyle", "dplyr", "DT", "ggplot2", "GO.db", "httr", "magritrr", "org.Hs.eg.db", "reactome.db", "readr", "rlang", "S4Vectors", "sigora", "slam", "tibble", "tidyr", "tidyverse", "UpSetR")

new_packages <- list_of_packages[!(list_of_packages %in% installed.packages()[,"Package"])]
if(length(new_packages)) install.packages(new_packages)

3.2 Windows:

Run the following in R:

install.packages("remotes")
library(remotes)
remotes::install_github("protViz/fgcz.gsea.ora", build_vignettes = FALSE)

For installing package together with vignettes run:

remotes::install_github("protViz/fgcz.gsea.ora", build_opts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE)

4. Vignettes

See fgcz.gsea.ora vignette:

vignette("fgcz.gsea.ora")

Vignette can also be found here:

https://rdrr.io/github/protViz/fgcz.gsea.ora/f/vignettes/vignette.Rmd