NEWS

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MetaboSignal 1.14.1

• MS_keggNetwork returns interaction subtype (e.g. activation) instead of type (e.g. PPrel). Thank you Shilpa Harshan for noticing this!

MetaboSignal 1.7.12

• MetaboSignal integrates KEGG metabolic and signaling networks with regulatory interactions reported in OmniPath and TRRUST.
• New functions: "MS2_ppiNetwork( )" and "MS2_mergeNetworks( )".

MetaboSignal 1.7.8

• MetaboSignal includes a new function: "MS_getPathIds()" which allows retrieving the identifiers (IDs) of all metabolic and signaling KEGG pathways of a given organism.
• "MS_keggNetwork()" can now transform KEGG IDs into Entrez gene IDs (use expand_genes = TRUE, convert_entrez = TRUE).
• "MS_filterNetwork()" has been renamed as "MS_topologyFilter".

MetaboSignal 1.7.2

• Major changes in function names:
• "MetaboSignal_matrix()" renamed as "MS_keggNetwork"
• "MetaboSignal_distances()" renamed as "MS_distances"
• "MetaboSignal_NetworkCytoscape()" renamed as "MS_shortestPathsNetwork"
• "MS_ToCytoscape()” renamed as "MS_exportCytoscape"
• "MS_ChangeNames()" renamed as "MS_changeNames"
• "MS_FilterNetwork()" renamed as "MS_filterNetwork"
• "MS_FindKEGG()" renamed as "MS_keggFinder"
• "MS_GetKEGG_GeneID" renamed as "MS_convertGene"
• "MS_NodeBW()" renamed as "MS_nodeBW"
• "MS_ReplaceNode()" renamed as "MS_replaceNode"
• "MS_RemoveNode()" renamed as "MS_removeNode"
• "MS_FindMappedNodes()" renamed as "MS_findMappedNodes"
• New functions:
• "MS_tissueFilter()": allows filtering a network based on tissue expression data.
• Functions removed:
• "MS_interactionType()": interactions can be now retrieved directly from MS_keggNetwork.
• Functionality changes:
• "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.
• "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.

MetaboSignal 1.7.1

• Significant improvements in the tissue-filtering option from "MetaboSignal_matrix()".
• Cytoscape .txt files are now exported with a header.

MetaboSignal 1.1.6

• 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()".
• "MS_GetShortestpaths()" has been modified and now the output shortest path(s) can be represented as a network-table (i.e. 2-column matrix).