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

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.

AuthorAristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos
Date of publication
MaintainerPanos Balomenos <balomenos@upatras.gr>
LicenseGPL-2
Version1.2.0

View on Bioconductor

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

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