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Metabolic Pathway Analysis of RNA

Bioconductor version: Release (3.19)

MetaPhOR was developed to enable users to assess metabolic dysregulation using transcriptomic-level data (RNA-sequencing and Microarray data) and produce publication-quality figures. A list of differentially expressed genes (DEGs), which includes fold change and p value, from DESeq2 or limma, can be used as input, with sample size for MetaPhOR, and will produce a data frame of scores for each KEGG pathway. These scores represent the magnitude and direction of transcriptional change within the pathway, along with estimated p-values.MetaPhOR then uses these scores to visualize metabolic profiles within and between samples through a variety of mechanisms, including: bubble plots, heatmaps, and pathway models.

Author: Emily Isenhart [aut, cre], Spencer Rosario [aut]

Maintainer: Emily Isenhart <emily.isenhart at>

Citation (from within R, enter citation("MetaPhOR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

MetaPhOR HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3
System Requirements Cytoscape (>= 3.9.0) for the cytoPath() examples
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Follow Installation instructions to use this package in your R session.

Source Package MetaPhOR_1.6.0.tar.gz
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macOS Binary (x86_64) MetaPhOR_1.6.0.tgz
macOS Binary (arm64) MetaPhOR_1.6.0.tgz
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