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

## Documentation for package ‘MetaboSignal’ version 1.4.0

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

## Help Pages

directionality_reactions | List of KEGG reactions with incorrect/inconsistent directionality
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 expression
MetaboSignal_tableUnfiltered | Example of MetaboSignal network-table unfiltered by tissue expression
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