CHRONOS: A time-varying method for microRNA-mediated sub-pathway
enrichment analysis
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Documentation for package ‘CHRONOS’ version 1.34.0
Help Pages
| 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) |