Package: MetaPhOR Type: Package Title: Metabolic Pathway Analysis of RNA Version: 1.15.0 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 cmake libfontconfig1-dev libfreetype6-dev libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3 libzmq3-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:59:12 UTC RemoteUrl: https://github.com/bioc/MetaPhOR RemoteRef: HEAD RemoteSha: dbe96ea8cd46a7bdb554701c0b4fffacacb1e28f NeedsCompilation: no Packaged: 2026-07-04 22:45:49 UTC; root Author: Emily Isenhart [aut, cre], Spencer Rosario [aut] Maintainer: Emily Isenhart