EMMA
This is the development version of EMMA; to use it, please install the devel version of Bioconductor.
EMMA: Enrichment Methods Matter for enabling fully reproducible and provenance-aware pathway analysis
Bioconductor version: Development (3.24)
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.
Author: Najla Abassi [aut, cre]
, Annekathrin Nedwed [aut]
, Federico Marini [aut]
Maintainer: Najla Abassi <abassi.nejla96 at gmail.com>
citation("EMMA")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("EMMA")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("EMMA")| EMMA | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, KEGG, Pathways, SingleCell, Software, Transcriptomics |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | AnnotationDbi, cli |
| System Requirements | |
| URL | https://github.com/imbeimainz/EMMA |
| Bug Reports | https://github.com/imbeimainz/EMMA/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, macrophage, DESeq2, apeglm, clusterProfiler, gprofiler2, org.Hs.eg.db, GO.db, mosdef, topGO, renv, DeeDeeExperiment, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EMMA_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | EMMA_0.99.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/EMMA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EMMA |
| Bioc Package Browser | https://code.bioconductor.org/browse/EMMA/ |
| Package Short Url | https://bioconductor.org/packages/EMMA/ |
| Package Downloads Report | Download Stats |