Package: enrichmet 0.99.18

Yonatan Mekonnen

enrichmet: enrichmet: R package for Quick and Easy Pathway and Network Analyses in Metabolomics

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.

Authors:Yonatan Mekonnen [aut, cre], H. Lee Moffitt Cancer Center & Research Institute [fnd]

enrichmet_0.99.18.tar.gz
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enrichmet_0.99.18.tgz(r-4.6-any)enrichmet_0.99.18.tgz(r-4.5-any)
enrichmet_0.99.18.tar.gz(r-4.7-any)enrichmet_0.99.18.tar.gz(r-4.6-any)
enrichmet_0.99.18.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
enrichmet/json (API)

# Install 'enrichmet' in R:

install.packages('enrichmet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biodatalab/enrichmet/issues

On CRAN:

metabolomics pathways network networkenrichment kegg visualization

2.78 score 2 stars 8 scripts 25 exports 111 dependencies

Last updated from:3141d808a3. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	192
linux-devel	OK	505
source / vignettes	OK	300
linux-release	OK	515
macos-release	OK	361
macos-oldrel	OK	526
windows-devel	OK	316
windows-release	OK	380
windows-oldrel	OK	369
wasm-release	OK	162

Exports:calculate_metabolite_centrality create_centrality_plot create_enrichment_plot create_gsea_plot create_heatmap_plot create_impact_plot create_interaction_plot create_membership_plot create_network_plot da_results_from_se enrichmet extract_kegg_ids extract_measured_kegg_ids fetch_kegg_chebi fetch_kegg_compound_lookup fetch_kegg_pathway_metabolites fetch_kegg_reactome fetch_lion_lipid_ontology fetch_reactome_reactions get_cached_file perform_enrichment_analysis perform_enrichment_analysis_bg perform_gsea_analysis prepare_gmt_data run_de

Dependencies:abind askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 blob cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray digest doParallel dplyr farver fastmap fastmatch fgsea filelock foreach formatR futile.logger futile.options generics GenomicRanges GetoptLong ggforce ggplot2 ggraph ggrepel GlobalOptions glue graphlayouts gridExtra gtable httr2 igraph IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise openssl openxlsx pillar pkgconfig plyr png polyclip purrr qvalue R6 RColorBrewer Rcpp RcppArmadillo reshape2 rjson rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr XVector zip

enrichmet: Pathway and Network Analysis for Metabolomics Tutorial

Rendered fromTutorial.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2025-05-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Metabolite Centrality	calculate_metabolite_centrality
Create Centrality Plot	create_centrality_plot
Create Pathway Enrichment Plot	create_enrichment_plot
Create GSEA Plot	create_gsea_plot
Create Enrichment Heatmap	create_heatmap_plot
Create Impact vs Significance Plot	create_impact_plot
Create Metabolite Interaction Network (Reactome)	create_interaction_plot
Create Pathway Membership Plot	create_membership_plot
Create Metabolite Pathway Network	create_network_plot
Convert a SummarizedExperiment to a da_results Object	da_results_from_se
ENRICHMET: Comprehensive Pathway Analysis for Metabolomics Data	enrichmet
Extract KEGG compound IDs from pathway data	extract_kegg_ids
Extract measured KEGG metabolite IDs from a summary statistics table	extract_measured_kegg_ids
Fetch KEGG-ChEBI mappings	fetch_kegg_chebi
Fetch KEGG compound names	fetch_kegg_compound_lookup
Fetch KEGG pathway-metabolite relationships	fetch_kegg_pathway_metabolites
Build KEGG-Reactome reaction mappings	fetch_kegg_reactome
Fetch LION lipid ontology	fetch_lion_lipid_ontology
Fetch Reactome reactions	fetch_reactome_reactions
Download and cache a remote file	get_cached_file
Perform Pathway Enrichment Analysis	perform_enrichment_analysis
Perform pathway enrichment with optional background correction	perform_enrichment_analysis_bg
Perform GSEA-style Pathway Enrichment Analysis	perform_gsea_analysis
Prepare GMT Data for Pathway Analysis	prepare_gmt_data
Run Differential Expression Analysis using LIMMA	run_de