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

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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.

Author
Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos
Date of publication
Maintainer
Panos Balomenos <balomenos@upatras.gr>
License
GPL-2
Version
1.2.0

View on Bioconductor

Man pages

CHRONOSrun
Default run of CHRONOS
convertMiRNANomenclature
Conform miRNA annotations to the ones currently used by...
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...
importExpressions
Import gene and miRNA expressions from
pathwayMeasures
Pathway structural and functional aspects
scoreSubpathways
Evaluate subpathways using an interacting scorng scheme (IS)...
subpathwayKEGGmap
Create links to KEGG pathway map with highlighted...
subpathwayMiRNAs
Create a circulat plot of a subpathway and the miRNAs that...
visualizeResults
Visualize results in tabular form (txt, xlsx)

Files in this package

CHRONOS/DESCRIPTION
CHRONOS/NAMESPACE
CHRONOS/R
CHRONOS/R/CHRONOSrun.R
CHRONOS/R/dataImport.R
CHRONOS/R/mRNAconversion.R
CHRONOS/R/miRNAconversion.R
CHRONOS/R/miRNAdownload.R
CHRONOS/R/pathwayAnalysis.R
CHRONOS/R/pathwayDownload.R
CHRONOS/R/pathwayMeasures.R
CHRONOS/R/pathwayToGraph.R
CHRONOS/R/subExtractionLinear.R
CHRONOS/R/subExtractionNonLinear.R
CHRONOS/R/subRefinement.R
CHRONOS/R/subScores.R
CHRONOS/R/subStatistics.R
CHRONOS/R/subVisualization.R
CHRONOS/R/utilities.R
CHRONOS/R/zzz.R
CHRONOS/build
CHRONOS/build/vignette.rds
CHRONOS/inst
CHRONOS/inst/CITATION
CHRONOS/inst/NEWS
CHRONOS/inst/doc
CHRONOS/inst/doc/CHRONOS.R
CHRONOS/inst/doc/CHRONOS.Rmd
CHRONOS/inst/doc/CHRONOS.pdf
CHRONOS/inst/extdata
CHRONOS/inst/extdata/Downloads
CHRONOS/inst/extdata/Downloads/KEGG
CHRONOS/inst/extdata/Downloads/KEGG/hsa
CHRONOS/inst/extdata/Downloads/KEGG/hsa/hsa04915.xml
CHRONOS/inst/extdata/Downloads/KEGG/hsa/hsa04917.xml
CHRONOS/inst/extdata/Downloads/KEGG/hsa/hsa04930.xml
CHRONOS/inst/extdata/Downloads/KEGG/hsa/hsa05031.xml
CHRONOS/inst/extdata/Downloads/mirbase
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_cel.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_cfa.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_dme.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_dre.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_gga.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_hsa.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_mmu.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_oar.RData
CHRONOS/inst/extdata/Downloads/mirbase/miRNAmaps_rno.RData
CHRONOS/inst/extdata/Examples
CHRONOS/inst/extdata/Examples/data.RData
CHRONOS/inst/extdata/Examples/kgml
CHRONOS/inst/extdata/Examples/kgml/hsa04915.xml
CHRONOS/inst/extdata/Examples/kgml/hsa04917.xml
CHRONOS/inst/extdata/Examples/kgml/hsa04930.xml
CHRONOS/inst/extdata/Examples/kgml/hsa05031.xml
CHRONOS/inst/extdata/User
CHRONOS/inst/extdata/User/TarBase.xlsx
CHRONOS/inst/extdata/User/interestingGenes.txt
CHRONOS/inst/extdata/User/mRNAexpressions.txt
CHRONOS/inst/extdata/User/miRNAexpressions.txt
CHRONOS/inst/extdata/User/miRecords.xlsx
CHRONOS/inst/java
CHRONOS/inst/java/CHRONOS.jar
CHRONOS/inst/unitTests
CHRONOS/inst/unitTests/test_CHRONOSrun.R
CHRONOS/inst/unitTests/test_pathwayToGraph.R
CHRONOS/inst/unitTests/test_subExtractionLinear.R
CHRONOS/inst/unitTests/test_subExtractionNonLinear.R
CHRONOS/inst/unitTests/test_subRefinement.R
CHRONOS/inst/unitTests/test_subVisualization.R
CHRONOS/java
CHRONOS/java/FileIO.java
CHRONOS/java/Graph.java
CHRONOS/java/LinearPaths.java
CHRONOS/man
CHRONOS/man/CHRONOSrun.Rd
CHRONOS/man/convertMiRNANomenclature.Rd
CHRONOS/man/convertNomenclature.Rd
CHRONOS/man/createPathwayGraphs.Rd
CHRONOS/man/downloadKEGGPathwayList.Rd
CHRONOS/man/downloadMiRecords.Rd
CHRONOS/man/downloadPathways.Rd
CHRONOS/man/extractLinearSubpathways.Rd
CHRONOS/man/extractNonLinearSubpathways.Rd
CHRONOS/man/getEdgeTypes.Rd
CHRONOS/man/importExpressions.Rd
CHRONOS/man/pathwayMeasures.Rd
CHRONOS/man/scoreSubpathways.Rd
CHRONOS/man/subpathwayKEGGmap.Rd
CHRONOS/man/subpathwayMiRNAs.Rd
CHRONOS/man/visualizeResults.Rd
CHRONOS/tests
CHRONOS/tests/runTests.R
CHRONOS/vignettes
CHRONOS/vignettes/CHRONOS.Rmd
CHRONOS/vignettes/figures
CHRONOS/vignettes/figures/results.png