DOI: 10.18129/B9.bioc.MetaPhOR  

This is the development version of MetaPhOR; for the stable release version, see MetaPhOR.

Metabolic Pathway Analysis of RNA

Bioconductor version: Development (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>

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biocViews DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version 1.5.0
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
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