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) |