Package: MetaPhOR
Type: Package
Title: Metabolic Pathway Analysis of RNA
Version: 1.11.0
Authors@R: 
    c(person("Emily", "Isenhart", email = "emily.isenhart@roswellpark.org",
        role = c("aut", "cre")),
    person("Spencer", "Rosario",role = "aut"))
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 7.2.1
Imports: utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
        clusterProfiler, RecordLinkage, RCy3
Depends: R (>= 4.2.0)
biocViews: Metabolomics, RNASeq, Pathways, GeneExpression,
        DifferentialExpression, KEGG, Sequencing, Microarray
Suggests: BiocStyle, knitr, rmarkdown, kableExtra
VignetteBuilder: knitr
SystemRequirements: Cytoscape (>= 3.9.0) for the cytoPath() examples
git_url: https://git.bioconductor.org/packages/MetaPhOR
git_branch: devel
git_last_commit: cf1b531
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 00:31:10 UTC; biocbuild
Author: Emily Isenhart [aut, cre],
  Spencer Rosario [aut]
Maintainer: Emily Isenhart <emily.isenhart@roswellpark.org>
Built: R 4.5.0; ; 2025-06-05 13:22:21 UTC; windows
