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CHRONOS (version 1.0.3)

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

Description

A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

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Version

Version

1.0.3

License

GPL-2

Maintainer

Panos Balomenos

Last Published

February 15th, 2017

Functions in CHRONOS (1.0.3)

createPathwayGraphs

Convert KEGG Pathways to Gene-Gene Network Graphs.
downloadKEGGPathwayList

Retrieve all availiable pathways for an organism.
convertNomenclature

Convert genes identifier nomenclature.
subpathwayMiRNAs

Create a circulat plot of a subpathway and the miRNAs that target it.
downloadPathways

Download KEGG pathways in KGML format.
CHRONOSrun

Default run of CHRONOS
importExpressions

Import gene and miRNA expressions from
extractNonLinearSubpathways

Non linear subpathway extraction from pathway graphs
extractLinearSubpathways

Linear subpathway extraction from pathway graphs
scoreSubpathways

Evaluate subpathways using an interacting scorng scheme (IS) for each time point.
pathwayMeasures

Pathway structural and functional aspects
visualizeResults

Visualize results in tabular form (txt, xlsx)
getEdgeTypes

Map various types of gene-gene interactions in KGML files to edge types in corresponding pathway graphs.
convertMiRNANomenclature

Conform miRNA annotations to the ones currently used by miRecords.
subpathwayKEGGmap

Create links to KEGG pathway map with highlighted subpathways.
downloadMiRecords

Download miRNA-mRNA interactions for an organism.