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.
|Author||Andrea Rodriguez-Martinez <email@example.com>, Rafael Ayala <firstname.lastname@example.org>, Joram M. Posma <email@example.com>, Ana L. Neves <firstname.lastname@example.org>, Marc-Emmanuel Dumas <email@example.com>|
|Date of publication||None|
|Maintainer||Andrea Rodriguez-Martinez <firstname.lastname@example.org>, Rafael Ayala <email@example.com>|
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_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