Package: MetaPhOR 1.9.0
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:
MetaPhOR_1.9.0.tar.gz
MetaPhOR_1.9.0.zip(r-4.5)MetaPhOR_1.9.0.zip(r-4.4)MetaPhOR_1.9.0.zip(r-4.3)
MetaPhOR_1.9.0.tgz(r-4.4-any)MetaPhOR_1.9.0.tgz(r-4.3-any)
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MetaPhOR.pdf |MetaPhOR.html✨
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-1.9.0(bioc 3.21)MetaPhOR-1.8.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
metabolomicsrnaseqpathwaysgeneexpressiondifferentialexpressionkeggsequencingmicroarray
Last updated 25 days agofrom:ffbf2ed04a. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | OK | Nov 18 2024 |
| R-4.5-linux | OK | Nov 18 2024 |
| R-4.4-win | OK | Nov 18 2024 |
| R-4.4-mac | OK | Nov 18 2024 |
| R-4.3-win | OK | Nov 18 2024 |
| R-4.3-mac | OK | Nov 18 2024 |
Exports:bubblePlotcytoPathmetaHeatmappathwayAnalysispathwayList
Dependencies:adaAnnotationDbiapeaplotaskpassbackportsbase64encbase64urlBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclasscliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdiagramdigestDOSEdplyre1071enrichplotevaluateevdfansifarverfastmapfastmatchfffgseaformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglobalsglueGO.dbGOSemSimgplotsgraphgridGraphicsgsongtablegtoolshtmltoolshttrigraphipredIRangesIRdisplayIRkernelisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelavalazyevallifecyclelistenvmagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetnumDerivopensslparallellypatchworkpbdZMQpheatmappillarpkgconfigplogrplyrpngpolyclipprodlimprogressrproxypurrrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenRCurlRCy3RecordLinkagereprreshape2RJSONIOrlangrpartRSQLiteS4VectorsscalesscatterpieshapesnowSQUAREMstringistringrsurvivalsyssystemfontstibbletidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8uuidvctrsviridisLitewithrXMLxtableXVectoryulab.utilszlibbioc
Readme and manuals
Help Manual
| 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 |
