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

Functions

CHRONOSrun Man page
convertMiRNANomenclature Man page
convertNomenclature Man page
createPathwayGraphs Man page
downloadKEGGPathwayList Man page
downloadMiRecords Man page
downloadPathways Man page
extractLinearSubpathways Man page
extractNonLinearSubpathways Man page
getEdgeTypes Man page
importExpressions Man page
pathwayMeasures Man page
scoreSubpathways Man page
subpathwayKEGGmap Man page
subpathwayMiRNAs Man page
visualizeResults Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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