Package: MetaPhOR
Type: Package
Title: Metabolic Pathway Analysis of RNA
Version: 1.12.0
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
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libxml2-dev libssl-dev
        python3 libzmq3-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:19:21 UTC
RemoteUrl: https://github.com/bioc/MetaPhOR
RemoteRef: RELEASE_3_22
RemoteSha: ef1fc186f62acff4b5cc8969b85faa29adb7cff0
NeedsCompilation: no
Packaged: 2026-03-03 09:15:18 UTC; root
Author: Emily Isenhart [aut, cre],
  Spencer Rosario [aut]
Maintainer: Emily Isenhart <emily.isenhart@roswellpark.org>
Built: R 4.5.2; ; 2026-03-03 09:17:45 UTC; windows
