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.

Author
Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13@imperial.ac.uk>, Rafael Ayala <r.ayala14@imperial.ac.uk>, Joram M. Posma <j.posma11@imperial.ac.uk>, Ana L. Neves <ana.luisa.neves14@imperial.ac.uk>, Marc-Emmanuel Dumas <m.dumas@imperial.ac.uk>
Date of publication
None
Maintainer
Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13@imperial.ac.uk>, Rafael Ayala <r.ayala14@imperial.ac.uk>
License
GPL-3
Version
1.4.0

View on Bioconductor

Man pages

directionality_reactions
List of KEGG reactions with incorrect/inconsistent...
hpaNormalTissue
Expression profiles for proteins in human tissues
MetaboSignal_distances
Calculate gene-metabolite distance matrix
MetaboSignal_matrix
Build MetaboSignal network-table
MetaboSignal_NetworkCytoscape
Build shortest-path subnetwork
MetaboSignal_table
Example of MetaboSignal network-table filtered by tissue...
MetaboSignal_tableUnfiltered
Example of MetaboSignal network-table unfiltered by tissue...
MS_ChangeNames
Transform KEGG IDs into common names
MS_FilterNetwork
Filter network based on distances or betweenness
MS_FindKEGG
Get KEGG IDs for compounds, organisms or pathways
MS_FindMappedNodes
Map gene IDs or metabolite IDs onto the network
MS_GetKEGG_GeneID
Transform entrez IDs or gene symbols into KEGG IDs
MS_GetShortestpaths
Calculate shortest paths
MS_NodeBW
Get distribution of node betweeness
MS_RemoveNode
Remove undesired nodes from the network
MS_ReplaceNode
Replace nodes of the network
MS_ToCytoscape
Export network in cytoscape format
neglected_genes
Genes removed during tissue-expression filtering
subnetwork
Shortest-path subnetwork

Files in this package

MetaboSignal/DESCRIPTION
MetaboSignal/MetaboSignal.Rproj
MetaboSignal/NAMESPACE
MetaboSignal/NEWS
MetaboSignal/R
MetaboSignal/R/Find_support_Functions.R
MetaboSignal/R/MetaboSignal_NetworkCytoscape.R
MetaboSignal/R/MetaboSignal_distances.R
MetaboSignal/R/MetaboSignal_matrix.R
MetaboSignal/R/Other_support_Functions.R
MetaboSignal/R/general_internal_functions.R
MetaboSignal/R/metabolic_matrix.R
MetaboSignal/R/signaling_matrix.R
MetaboSignal/README.md
MetaboSignal/build
MetaboSignal/build/vignette.rds
MetaboSignal/data
MetaboSignal/data/MetaboSignal_table.rda
MetaboSignal/data/MetaboSignal_tableUnfiltered.rda
MetaboSignal/data/directionality_reactions.rda
MetaboSignal/data/hpaNormalTissue.rda
MetaboSignal/data/neglected_genes.rda
MetaboSignal/data/subnetwork.rda
MetaboSignal/inst
MetaboSignal/inst/doc
MetaboSignal/inst/doc/MetaboSignal.R
MetaboSignal/inst/doc/MetaboSignal.Rmd
MetaboSignal/inst/doc/MetaboSignal.html
MetaboSignal/inst/unitTests
MetaboSignal/inst/unitTests/test_MetaboSignal.R
MetaboSignal/man
MetaboSignal/man/MS_ChangeNames.Rd
MetaboSignal/man/MS_FilterNetwork.Rd
MetaboSignal/man/MS_FindKEGG.Rd
MetaboSignal/man/MS_FindMappedNodes.Rd
MetaboSignal/man/MS_GetKEGG_GeneID.Rd
MetaboSignal/man/MS_GetShortestpaths.Rd
MetaboSignal/man/MS_NodeBW.Rd
MetaboSignal/man/MS_RemoveNode.Rd
MetaboSignal/man/MS_ReplaceNode.Rd
MetaboSignal/man/MS_ToCytoscape.Rd
MetaboSignal/man/MetaboSignal_NetworkCytoscape.Rd
MetaboSignal/man/MetaboSignal_distances.Rd
MetaboSignal/man/MetaboSignal_matrix.Rd
MetaboSignal/man/MetaboSignal_table.Rd
MetaboSignal/man/MetaboSignal_tableUnfiltered.Rd
MetaboSignal/man/directionality_reactions.Rd
MetaboSignal/man/hpaNormalTissue.Rd
MetaboSignal/man/neglected_genes.Rd
MetaboSignal/man/subnetwork.Rd
MetaboSignal/tests
MetaboSignal/tests/runTests.R
MetaboSignal/vignettes
MetaboSignal/vignettes/MetaboSignal.Rmd
MetaboSignal/vignettes/figures
MetaboSignal/vignettes/figures/network.jpg
MetaboSignal/vignettes/knitcitations.bib
MetaboSignal/vignettes/mystyle.css
MetaboSignal/vignettes/template.csl