EMMA

EMMA: Enrichment Methods Matter for enabling fully reproducible and provenance-aware pathway analysis

Bioconductor version: 3.24 · Package version: 0.99.5

EMMA is a package that provides a provenance-aware execution framework for functional enrichment analyses. It allows users to run enrichment analyses using existing tools and workflows while explicitly capturing analytical parameters during runtime, and returns the native enrichment results output together with structured metadata.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EMMA")

Details

Maintainer	Najla Abassi <abassi.nejla96@gmail.com>
Author	Najla Abassi [aut, cre] (ORCID: <https://orcid.org/0000-0001-8357-0938>), Annekathrin Nedwed [aut] (ORCID: <https://orcid.org/0000-0002-2475-4945>), Federico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>)
License	MIT + file LICENSE
URL	https://github.com/imbeimainz/EMMA
Bug Reports	https://github.com/imbeimainz/EMMA/issues
Downloads rank	66
Source branch	devel
biocViews	DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, KEGG, Pathways, SingleCell, Software, Transcriptomics

Documentation

The EMMA User's Guide - Enrichment Method MAtters

Download

Follow the installation instructions to use this package in your R session.

Source package	EMMA_0.99.5.tar.gz
Windows binary (x86_64)	EMMA_0.99.5.zip
macOS binary (arm64)	EMMA_0.99.5.tgz
macOS binary (x86_64)	EMMA_0.99.5.tgz

Dependencies

Depends: R (>= 4.1.0)

Imports: AnnotationDbi, cli

Suggests: knitr, rmarkdown, BiocStyle, macrophage, DESeq2, apeglm, clusterProfiler, gprofiler2, org.Hs.eg.db, GO.db, mosdef, topGO, renv, DeeDeeExperiment, testthat (>= 3.0.0)