MetaPhOR
This is the released version of MetaPhOR; for the devel version, see MetaPhOR.
Metabolic Pathway Analysis of RNA
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | MetaPhOR_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | MetaPhOR_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | MetaPhOR_1.14.0.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 |