CHANGES IN VERSION 1.14.1 ----------------------- o MS_keggNetwork returns interaction subtype (e.g. activation) instead of type (e.g. PPrel). Thank you Shilpa Harshan for noticing this! CHANGES IN VERSION 1.7.12 ----------------------- o MetaboSignal integrates KEGG metabolic and signaling networks with regulatory interactions reported in OmniPath and TRRUST. o New functions: "MS2_ppiNetwork( )" and "MS2_mergeNetworks( )". CHANGES IN VERSION 1.7.8 ----------------------- o MetaboSignal includes a new function: "MS_getPathIds()" which allows retrieving the identifiers (IDs) of all metabolic and signaling KEGG pathways of a given organism. o "MS_keggNetwork()" can now transform KEGG IDs into Entrez gene IDs (use expand_genes = TRUE, convert_entrez = TRUE). o "MS_filterNetwork()" has been renamed as "MS_topologyFilter". CHANGES IN VERSION 1.7.2 ----------------------- o Major changes in function names: o "MetaboSignal_matrix()" renamed as "MS_keggNetwork" o "MetaboSignal_distances()" renamed as "MS_distances" o "MetaboSignal_NetworkCytoscape()" renamed as "MS_shortestPathsNetwork" o "MS_ToCytoscape()” renamed as "MS_exportCytoscape" o "MS_ChangeNames()" renamed as "MS_changeNames" o "MS_FilterNetwork()" renamed as "MS_filterNetwork" o "MS_FindKEGG()" renamed as "MS_keggFinder" o "MS_GetKEGG_GeneID" renamed as "MS_convertGene" o "MS_NodeBW()" renamed as "MS_nodeBW" o "MS_ReplaceNode()" renamed as "MS_replaceNode" o "MS_RemoveNode()" renamed as "MS_removeNode" o "MS_FindMappedNodes()" renamed as "MS_findMappedNodes" o New functions: o "MS_tissueFilter()": allows filtering a network based on tissue expression data. o Functions removed: o "MS_interactionType()": interactions can be now retrieved directly from MS_keggNetwork. o Functionality changes: o "MS_keggNetwork()": output networks are now formatted as 3-column matrices, where the third column indicates interaction type. Unlike, MetaboSignal_matrix, “MS_keggNetwork()" does not perform network filtering by tissue expression data. Tissue filtering is now done with "MS_tissueFilter()". Also, the compound nodes of the networks are not only metabolites, but also drugs and glycans. o "MS_distances()", "MS_shortestPathNetworks()": use network nodes (i.e. KEGG IDs) as source nodes, not entrez IDs or gene symbols. However, the function "MS_convertGene()" allows to easily convert entrez IDs or gene symbols into KEGG IDs. CHANGES IN VERSION 1.7.1 ----------------------- o Significant improvements in the tissue-filtering option from "MetaboSignal_matrix()". o Cytoscape .txt files are now exported with a header. CHANGES IN VERSION 1.1.6 ----------------------- o MetaboSignal includes a new function: "MS_interactionType()". This function allows getting the interaction subtype between signaling nodes. The output matrix generated by this function can be used for "MetaboSignal_NetworkCytoscape()" and also for "MS_GetShortestpaths()". o "MS_GetShortestpaths()" has been modified and now the output shortest path(s) can be represented as a network-table (i.e. 2-column matrix).