Package: MetaboSignal 1.37.0

Andrea Rodriguez-Martinez

MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

Authors:Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas

MetaboSignal_1.37.0.tar.gz
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MetaboSignal.pdf |MetaboSignal.html✨
MetaboSignal/json (API)
NEWS

# Install 'MetaboSignal' in R:
install.packages('MetaboSignal', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:MetaboSignal-1.35.0(bioc 3.20)MetaboSignal-1.34.0(bioc 3.19)

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

graphandnetworkgenesignalinggenetargetnetworkpathwayskeggreactomesoftware

5.08 score 5 scripts 300 downloads 4 mentions 19 exports 188 dependencies

Last updated 23 days agofrom:3fa4cf5f16. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winNOTEOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:MS_changeNamesMS_convertGeneMS_distancesMS_exportCytoscapeMS_findMappedNodesMS_getPathIdsMS_keggFinderMS_keggNetworkMS_nodeBWMS_reactionNetworkMS_removeDrugsMS_removeNodeMS_replaceNodeMS_shortestPathsMS_shortestPathsNetworkMS_tissueFilterMS_topologyFilterMS2_mergeNetworksMS2_ppiNetwork

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacheckmatechroncirclizecliclueclustercodetoolscolorspaceComplexHeatmapcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdigestdoBydoParalleldplyrEnsDb.Hsapiens.v75ensembldbevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggplot2glm2GlobalOptionsgluegraphgridExtragsubfngtablehighrHmischmshparhtmlTablehtmltoolshtmlwidgetshttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGgraphKEGGRESTknitrlabelinglambda.rlatticelazyevallifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellMWASToolsmygenenlmenloptrnnetnumDerivopensslorg.Hs.eg.dbpbkrtestpillarpkgconfigplogrplyrpngppcorprettyunitsprogressProtGenericsprotopurrrquantregqvalueR6rappdirsRColorBrewerRcppRcppEigenRCurlreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesshapesnowSparseArraySparseMsqldfstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc

MetaboSignal

Rendered fromMetaboSignal.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2017-09-19
Started: 2016-09-12

MetaboSignal 2: merging KEGG with additional interaction resources

Rendered fromMetaboSignal2.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2017-09-19
Started: 2017-09-13

Readme and manuals

Help Manual

Help pageTopics
List of KEGG reactions with incorrect/inconsistent directionalitydirectionality_reactions
Expression profiles for proteins in human tissueshpaNormalTissue
Examples of metabolic and signaling human KEGG pathwayskegg_pathways
KEGG network examplekeggNet_example
Network containing KEGG, OmniPath and TRRUST interactionsmergedNet_example
Example of MetaboSignal network-tableMetaboSignal_table
Transform KEGG IDs into common namesMS_changeNames
Transform Entrez IDs or gene symbols into KEGG IDsMS_convertGene
Calculate gene-metabolite distance matrixMS_distances
Export network in cytoscape formatMS_exportCytoscape
Map gene IDs or metabolite IDs onto the networkMS_findMappedNodes
Get pathway identifiers of a given organismMS_getPathIds
Get KEGG IDs for compounds, organisms or pathwaysMS_keggFinder
Build MetaboSignal network-tableMS_keggNetwork
Get distribution of node betweenessMS_nodeBW
Build reaction-compound networkMS_reactionNetwork
Remove edges containing drug nodesMS_removeDrugs
Remove undesired nodes from the networkMS_removeNode
Replace nodes of the networkMS_replaceNode
Calculate shortest pathsMS_shortestPaths
Build shortest-path subnetworkMS_shortestPathsNetwork
Filter network based on tissue expression dataMS_tissueFilter
Filter network based on distances or betweennessMS_topologyFilter
Merge networksMS2_mergeNetworks
Build signaling-transduction networkMS2_ppiNetwork
Signaling-transduction networkppiNet_example
Regulatory interactions from OmniPath and TRRUSTregulatory_interactions