Package: MetaPhOR 1.7.0

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]

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Peer review:

On BioConductor:MetaPhOR-1.7.0(bioc 3.20)MetaPhOR-1.6.0(bioc 3.19)

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

bioconductor-package

5 exports 0.36 score 164 dependencies

Last updated 2 months agofrom:bd8ea30e3a

Exports:bubblePlotcytoPathmetaHeatmappathwayAnalysispathwayList

Dependencies:adaAnnotationDbiapeaplotaskpassbackportsbase64encbase64urlBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobcachemcaToolsclasscliclusterProfilercodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdiagramdigestDOSEdownloaderdplyre1071enrichplotevaluateevdfansifarverfastmapfastmatchfffgseaformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglobalsglueGO.dbGOSemSimgplotsgraphgraphlayoutsgridExtragridGraphicsgsongtablegtoolsHDO.dbhtmltoolshttrigraphipredIRangesIRdisplayIRkernelisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelavalazyevallifecyclelistenvmagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetnumDerivopensslparallellypatchworkpbdZMQpheatmappillarpkgconfigplogrplyrpngpolyclipprodlimprogressrproxypurrrqvalueR6RColorBrewerRcppRcppArmadilloRcppEigenRCurlRCy3RecordLinkagereprreshape2RJSONIOrlangrpartRSQLiteS4VectorsscalesscatterpieshadowtextshapesnowSQUAREMstringistringrsurvivalsyssystemfontstibbletidygraphtidyrtidyselecttidytreetreeiotweenrUCSC.utilsutf8uuidvctrsviridisviridisLitewithrXMLxtableXVectoryulab.utilszlibbioc