CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis


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Documentation for package ‘CHRONOS’ version 1.10.1

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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)