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

Documentation for package ‘MetaboSignal’ version 1.20.0

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