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


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Documentation for package ‘MetaboSignal’ version 1.4.0

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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