enrichmet
This is the development version of enrichmet; to use it, please install the devel version of Bioconductor.
enrichmet: R package for Quick and Easy Pathway and Network Analyses in Metabolomics
Bioconductor version: Development (3.24)
Provides functions to perform metabolite-based pathway enrichment analysis using Fisher's exact test and MetSEA. Computes relative betweenness centrality (RBC) of input metabolites in a pathway-metabolite interaction network. The package generates visualizations including pathway dot plots, MetSEA plots, metabolite centrality plots, and network plots. It supports KEGG-based pathway inputs and generates exportable results.
Author: Yonatan Mekonnen [aut, cre] 
, H. Lee Moffitt Cancer Center & Research Institute [fnd] (Grant number: P01CA250984)
Maintainer: Yonatan Mekonnen <yaayalew at gmail.com>
citation("enrichmet")):Yonatan Mekonnen. enrichmet: enrichmet: R package for Quick and Easy Pathway and Network Analyses in Metabolomics. doi:10.18129/B9.bioc.enrichmet, R package version 0.99.18, https://bioconductor.org/packages/enrichmet.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("enrichmet")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("enrichmet")| enrichmet: Pathway and Network Analysis for Metabolomics Tutorial | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | KEGG, Metabolomics, Network, NetworkEnrichment, Pathways, Software, Visualization |
| Version | 0.99.18 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | AGPL-3 + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocFileCache, methods, circlize, ComplexHeatmap, curl, data.table, dplyr, fgsea, ggplot2, ggraph, ggrepel, igraph, limma, openxlsx, qvalue, rlang, scales, stats, stringr, tibble, tidyr, utils, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/biodatalab/enrichmet |
| Bug Reports | https://github.com/biodatalab/enrichmet/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat (>= 3.2.0), withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/enrichmet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/enrichmet |
| Package Short Url | https://bioconductor.org/packages/enrichmet/ |
| Package Downloads Report | Download Stats |