CHRONOSrun              Default run of CHRONOS
convertMiRNANomenclature
                        Conform miRNA annotations to the ones currently
                        used by miRecords.
convertNomenclature     Convert genes identifier nomenclature.
createPathwayGraphs     Convert KEGG Pathways to Gene-Gene Network
                        Graphs.
downloadKEGGPathwayList
                        Retrieve all availiable pathways for an
                        organism.
downloadMiRecords       Download miRNA-mRNA interactions for an
                        organism.
downloadPathways        Download KEGG pathways in KGML format.
extractLinearSubpathways
                        Linear subpathway extraction from pathway
                        graphs
extractNonLinearSubpathways
                        Non linear subpathway extraction from pathway
                        graphs
getEdgeTypes            Map various types of gene-gene interactions in
                        KGML files to edge types in corresponding
                        pathway graphs.
importExpressions       Import gene and miRNA expressions from
pathwayMeasures         Pathway structural and functional aspects
scoreSubpathways        Evaluate subpathways using an interacting
                        scorng scheme (IS) for each time point.
subpathwayKEGGmap       Create links to KEGG pathway map with
                        highlighted subpathways.
subpathwayMiRNAs        Create a circulat plot of a subpathway and the
                        miRNAs that target it.
visualizeResults        Visualize results in tabular form (txt, xlsx)
