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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 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version 1.5.0
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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Suggests BiocStyle, knitr, rmarkdown, kableExtra
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Package Archives

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

Source Package MetaPhOR_1.5.0.tar.gz
Windows Binary MetaPhOR_1.5.0.zip
macOS Binary (x86_64) MetaPhOR_1.5.0.tgz
macOS Binary (arm64) MetaPhOR_1.5.0.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