EMMA - Enrichment Methods MAtter

EMMA enables the execution of Functional Enrichment Analyses using a wide range of existing tools (e.g. clusterProfiler, topGO, gprofiler2 among others) while systematically capturing analysis parameters and provenance information during runtime, and returning enrichment results in their standard format alongside structured and reusable metadata.

Installation

You can install the release version of EMMA from Bioconductor with:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")}

BiocManager::install("EMMA")

And the development version from GitHub with:

library("remotes")
remotes::install_github("imbeimainz/EMMA",
                        dependencies = TRUE,
                        build_vignettes = TRUE)

Example

library(EMMA)
# load data
data("de_res_IFNg_vs_naive", package = "EMMA")
data("gene_universe", package = "EMMA")

# run analysis
fea_results <- enrichGO(gene = rownames(de_res_IFNg_vs_naive),
                        universe = gene_universe,
                        keyType = "ENSEMBL",
                        OrgDb = org.Hs.eg.db,
                        ont = "BP") |> 
               EMMA_run()

Usage Overview

You can find the rendered version of the documentation of EMMA at the project website https://imbeimainz.github.io/EMMA/

Development

If you encounter a bug, have usage questions, or want to share ideas and functionality to make this package better, feel free to file an issue.

Code of Conduct

Please note that the EMMA project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

License

MIT