MetaPhOR

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see MetaPhOR.

Metabolic Pathway Analysis of RNA


Bioconductor version: 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 roswellpark.org>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DifferentialExpression, GeneExpression, KEGG, Metabolomics, Microarray, Pathways, RNASeq, Sequencing, Software
Version 1.4.0
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
URL
See More
Suggests BiocStyle, knitr, rmarkdown, kableExtra
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report 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 MetaPhOR_1.4.0.zip
macOS Binary (x86_64) MetaPhOR_1.4.0.tgz
macOS Binary (arm64) MetaPhOR_1.4.0.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