DOI: 10.18129/B9.bioc.MetaPhOR  

Metabolic Pathway Analysis of RNA

Bioconductor version: Release (3.18)

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 "4.3") 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:



HTML R Script MetaPhOR
PDF   Reference Manual
Text   NEWS


biocViews DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats, clusterProfiler, RecordLinkage, RCy3
Suggests BiocStyle, knitr, rmarkdown, kableExtra
SystemRequirements Cytoscape (>= 3.9.0) for the cytoPath() examples
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MetaPhOR_1.4.0.tar.gz
Windows Binary
macOS Binary (x86_64) MetaPhOR_1.4.0.tgz
macOS Binary (arm64) MetaPhOR_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: