MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
Version 1.6.0

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.

AuthorAndrea 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>
Bioconductor views GeneSignaling GeneTarget GraphAndNetwork KEGG Network Pathways Reactome Software
Date of publicationNone
MaintainerAndrea Rodriguez-Martinez <andrea.rodriguez-martinez13@imperial.ac.uk>, Rafael Ayala <r.ayala14@imperial.ac.uk>
LicenseGPL-3
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MetaboSignal")

Getting started

README.md

Popular man pages

MetaboSignal_matrix: Build MetaboSignal network-table
MetaboSignal_NetworkCytoscape: Build shortest-path subnetwork
MS_FilterNetwork: Filter network based on distances or betweenness
MS_FindKEGG: Get KEGG IDs for compounds, organisms or pathways
MS_GetKEGG_GeneID: Transform entrez IDs or gene symbols into KEGG IDs
MS_interactionType: Get interaction subtype
MS_NodeBW: Get distribution of node betweeness
See all...

All man pages Function index File listing

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_interactionType: Get interaction subtype
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
rno_pathways: Examples of metabolic and signaling rat KEGG pathways
subnetwork: Shortest-path subnetwork

Functions

ASP_paths Source code
BW_ranked_SP Source code
From_geneID_to_symbol Source code
MS_ChangeNames Man page Source code
MS_FilterNetwork Man page Source code
MS_FindCompound Source code
MS_FindKEGG Man page Source code
MS_FindMappedGenes Source code
MS_FindMappedMetabolites Source code
MS_FindMappedNodes Man page Source code
MS_FindOrganism Source code
MS_FindPathway Source code
MS_GetKEGG_GeneID Man page Source code
MS_GetShortestpaths Man page Source code
MS_NodeBW Man page Source code
MS_RemoveNode Man page Source code
MS_ReplaceNode Man page Source code
MS_ToCytoscape Man page Source code
MS_interactionType Man page Source code
Match Source code
MetaboSignal_NetworkCytoscape Man page Source code
MetaboSignal_distances Man page Source code
MetaboSignal_matrix Man page Source code
MetaboSignal_table Man page
MetaboSignal_tableUnfiltered Man page
add_reaction_edge Source code
bind_reaction_gene Source code
build_RG_edge Source code
build_signal_edges Source code
check_matrix Source code
check_mode_type Source code
check_unmapped Source code
collapse_interactions Source code
conv_entrez_kegg Source code
conv_entrez_symbol Source code
convertTable Source code
directionality_reactions Man page
filter_genes_tissue Source code
find_gene_metabo Source code
find_node_index Source code
find_unwanted_edge Source code
gene_SP Source code
get_bw_score Source code
get_global_BW_score Source code
get_interactiontype Source code
get_metabonet Source code
get_molecule_type Source code
get_signalnet Source code
get_target_type Source code
hpaNormalTissue Man page
igraph_edited Source code
link_hsagene_ensembl Source code
link_kogene Source code
link_reaction_gene Source code
match_KEGG Source code
match_interaction Source code
metabolic_matrix Source code
metabolite_SP Source code
neglected_genes Man page
network_features Source code
network_from_path Source code
new_edge Source code
orthology_clustering Source code
path_as_network Source code
rno_pathways Man page
signaling_matrix Source code
subnetwork Man page
unique_symbol_ensembl Source code

Files

DESCRIPTION
MetaboSignal.Rproj
NAMESPACE
NEWS
R
R/Find_support_Functions.R
R/MS_interactionType.R
R/MetaboSignal_NetworkCytoscape.R
R/MetaboSignal_distances.R
R/MetaboSignal_matrix.R
R/Other_support_Functions.R
R/general_internal_functions.R
R/metabolic_matrix.R
R/signaling_matrix.R
README.md
build
build/vignette.rds
data
data/MetaboSignal_table.rda
data/MetaboSignal_tableUnfiltered.rda
data/directionality_reactions.rda
data/hpaNormalTissue.rda
data/neglected_genes.rda
data/rno_pathways.rda
data/subnetwork.rda
inst
inst/CITATION
inst/doc
inst/doc/MetaboSignal.R
inst/doc/MetaboSignal.Rmd
inst/doc/MetaboSignal.html
inst/unitTests
inst/unitTests/test_MetaboSignal.R
man
man/MS_ChangeNames.Rd
man/MS_FilterNetwork.Rd
man/MS_FindKEGG.Rd
man/MS_FindMappedNodes.Rd
man/MS_GetKEGG_GeneID.Rd
man/MS_GetShortestpaths.Rd
man/MS_NodeBW.Rd
man/MS_RemoveNode.Rd
man/MS_ReplaceNode.Rd
man/MS_ToCytoscape.Rd
man/MS_interactionType.Rd
man/MetaboSignal_NetworkCytoscape.Rd
man/MetaboSignal_distances.Rd
man/MetaboSignal_matrix.Rd
man/MetaboSignal_table.Rd
man/MetaboSignal_tableUnfiltered.Rd
man/directionality_reactions.Rd
man/hpaNormalTissue.Rd
man/neglected_genes.Rd
man/rno_pathways.Rd
man/subnetwork.Rd
tests
tests/runTests.R
vignettes
vignettes/MetaboSignal.Rmd
vignettes/figures
vignettes/figures/network.jpg
vignettes/knitcitations.bib
vignettes/mystyle.css
vignettes/template.csl
MetaboSignal documentation built on May 20, 2017, 10:49 p.m.

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