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

## Documentation for package ‘MetaboSignal’ version 1.41.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

directionality_reactions | List of KEGG reactions with incorrect/inconsistent directionality
hpaNormalTissue | Expression profiles for proteins in human tissues
keggNet_example | KEGG network example
kegg_pathways | Examples of metabolic and signaling human KEGG pathways
mergedNet_example | Network containing KEGG, OmniPath and TRRUST interactions
MetaboSignal_table | Example of MetaboSignal network-table
MS2_mergeNetworks | Merge networks
MS2_ppiNetwork | Build signaling-transduction network
MS_changeNames | Transform KEGG IDs into common names
MS_convertGene | Transform Entrez IDs or gene symbols into KEGG IDs
MS_distances | Calculate gene-metabolite distance matrix
MS_exportCytoscape | Export network in cytoscape format
MS_findMappedNodes | Map gene IDs or metabolite IDs onto the network
MS_getPathIds | Get pathway identifiers of a given organism
MS_keggFinder | Get KEGG IDs for compounds, organisms or pathways
MS_keggNetwork | Build MetaboSignal network-table
MS_nodeBW | Get distribution of node betweeness
MS_reactionNetwork | Build reaction-compound network
MS_removeDrugs | Remove edges containing drug nodes
MS_removeNode | Remove undesired nodes from the network
MS_replaceNode | Replace nodes of the network
MS_shortestPaths | Calculate shortest paths
MS_shortestPathsNetwork | Build shortest-path subnetwork
MS_tissueFilter | Filter network based on tissue expression data
MS_topologyFilter | Filter network based on distances or betweenness
ppiNet_example | Signaling-transduction network
regulatory_interactions | Regulatory interactions from OmniPath and TRRUST