MetaPhOR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see MetaPhOR.
Metabolic Pathway Analysis of RNA
Bioconductor version: 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("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 | ||
| NEWS | Text |
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 |
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_1.6.0.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 |