MetaPhOR

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 roswellpark.org>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MetaPhOR")

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("MetaPhOR")

MetaPhOR	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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
URL

Suggests	BiocStyle, knitr, rmarkdown, kableExtra
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Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	MetaPhOR_1.6.0.tar.gz
Windows Binary (x86_64)	MetaPhOR_1.6.0.zip
macOS Binary (x86_64)	MetaPhOR_1.6.0.tgz
macOS Binary (arm64)	MetaPhOR_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MetaPhOR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MetaPhOR
Bioc Package Browser	https://code.bioconductor.org/browse/MetaPhOR/
Package Short Url	https://bioconductor.org/packages/MetaPhOR/
Package Downloads Report	Download Stats