Package: MetaPhOR 1.15.0

Emily Isenhart

MetaPhOR: Metabolic Pathway Analysis of RNA

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.

Authors:Emily Isenhart [aut, cre], Spencer Rosario [aut]

MetaPhOR_1.15.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MetaPhOR/json (API)

# Install 'MetaPhOR' in R:

install.packages('MetaPhOR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:MetaPhOR-1.15.0(bioc 3.24)MetaPhOR-1.14.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

metabolomics rnaseq pathways geneexpression differentialexpression kegg sequencing microarray

4.00 score 1 scripts 5 exports 164 dependencies

Last updated from:dbe96ea8cd. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	218
linux-devel-x86_64	OK	596
source / vignettes	OK	699
linux-release-x86_64	OK	594
macos-release-arm64	OK	353
macos-oldrel-arm64	OK	324
windows-devel	OK	585
windows-release	OK	584
windows-oldrel	OK	549
wasm-release	OK	222

Exports:bubblePlot cytoPath metaHeatmap pathwayAnalysis pathwayList

Dependencies:aisdk AnnotationDbi ape aplot askpass backports base64enc base64url Biobase BiocGenerics Biostrings bit bit64 bitops blob bslib cachem callr caTools class cli cluster clusterProfiler codetools cpp11 crayon curl data.table DBI diagram digest DOSE dplyr e1071 enrichit enrichplot evaluate evd farver fastmap ff fontawesome fontBitstreamVera fontLiberation fontquiver fs future future.apply gdtools generics ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree globals glue GO.db GOSemSim gplots graph gridGraphics gson gtable gtools highr htmltools htmlwidgets httr httr2 igraph ipred IRanges IRdisplay IRkernel isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice lava lazyeval lifecycle listenv magrittr MASS Matrix memoise mime nlme nnet numDeriv openssl otel parallelly patchwork pbdZMQ pheatmap pillar pkgconfig plyr png polyclip processx prodlim progressr proxy ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl RCy3 RecordLinkage repr reshape2 RJSONIO rlang rmarkdown rpart RSQLite S4Vectors S7 sass scales scatterpie Seqinfo shape SQUAREM stringi stringr survival sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 uuid vctrs viridisLite withr xfun XML xtable XVector yaml yulab.utils

MetaPhOR

Rendered fromMetaPhOR-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-10-17
Started: 2022-09-13

Help page	Topics
Create a Bubble Plot for Individual Samples	bubblePlot
Map Differentially Expressed Genes to Dysregulated Pathways	cytoPath
MetaPhOR: Metabolic Pathway Analysis of RNA	MetaPhOR-package MetaPhOR
Create a Heatmap for Comparing Multiple Samples	metaHeatmap
Metabolic Pathway Analysis of RNAseq Data	pathwayAnalysis
List Available Metabolic rWikiPathways	pathwayList

Package: MetaPhOR 1.15.0

MetaPhOR: Metabolic Pathway Analysis of RNA

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Help Manual

Usage by other packages (reverse dependencies)