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

## Documentation for package ‘CHRONOS’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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)