CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Version 1.4.0

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
Bioconductor views GraphAndNetwork KEGG Pathways SystemsBiology
Date of publication
MaintainerPanos Balomenos <balomenos@upatras.gr>
LicenseGPL-2
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CHRONOS")

Getting started

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

Popular man pages

CHRONOSrun: Default run of CHRONOS
createPathwayGraphs: Convert KEGG Pathways to Gene-Gene Network Graphs.
downloadKEGGPathwayList: Retrieve all availiable pathways 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...
See all...

All man pages Function index File listing

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)

Functions

CHRONOSrun Man page Source code
Sys.which2 Source code
betweennessCentrality Source code
bridgeness Source code
buildDirectories Source code
checkFile Source code
cleanDirectories Source code
cleanSubpath Source code
collapseSubpaths Source code
convertMiRNANomenclature Man page Source code
convertNomenclature Man page Source code
createDirectories Source code
createExcelOutputMulti Source code
createExcelOutputSingle Source code
createKEGGLink Source code
createKEGGLinks Source code
createMirnaLexicon Source code
createPathwayGraphs Man page Source code
createScoreFile Source code
degree Source code
doCirclize Source code
doSafeParallel Source code
downloadKEGGPathwayList Man page Source code
downloadMiRecords Man page Source code
downloadPathway Source code
downloadPathways Man page Source code Source code
evaluateSubpaths Source code
expandMetabolicGraph Source code
expandNonMetabolicGraph Source code
expandSubpath Source code
expansionEvaluator Source code
exportSubpaths Source code
exportToFile Source code
extractLinearSubpathways Man page Source code Source code
extractNonLinearSubpathways Man page Source code Source code
fillMatrixList Source code
filterExpressions Source code
filterLinearSubpaths Source code Source code
filterMatrix Source code
filterMiScores Source code
filterRecords Source code
filterSubScore Source code
fk Source code
fullCollapse Source code
getDoubleEdges Source code
getEdgeScores Source code
getEdgeTypes Man page Source code
getFilters Source code
getLengths Source code
getLinearPairs Source code
getLinearSubpath Source code
getMeasures Source code
getMiRNAtargetsUrl Source code
getMiRecordsData Source code
getMiRecordsMiRNAs Source code
getMiScores Source code
getPathwayType Source code
getProcessedData Source code
getSplittingFactor Source code
getStatistics Source code
getSubpathwayGenes Source code
getValMiRecordsTargets Source code
getValTarbaseTargets Source code
idxToMat Source code
importExpressions Man page Source code
importGeneExpressions Source code
importMiRNAExpressions Source code
importMiRNAFile Source code
indexSubpath Source code
mRNAconversion Source code
markov Source code
matrixToFile Source code
matrixToLexicon Source code
matrixToList Source code
metabolicPathwayToGraph Source code
miRNAsubScoring Source code
mirParser Source code
mirRenamer Source code
ndexSubpaths Source code
nlSubpaths Source code
nonMetabolicPathwayToGraph Source code
normalize Source code
onAttach Source code
onLoad Source code
onUnload Source code
optimalLengths Source code
pathwayMeasures Man page Source code
pathwayToGraph Source code
removeCompoundsMetabolicGraph Source code
removeCompoundsNonMetabolicGraph Source code
saveMiRNAFile Source code
scoreFCI Source code
scoreSubpaths Source code
scoreSubpathways Man page Source code Source code
scoreTVI Source code
splitWork Source code
subpathExpansion Source code
subpathwayKEGGmap Man page Source code
subpathwayMiRNAs Man page Source code
uniquifySubpaths Source code
unlistToMatrix Source code
visualizeResults Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/CHRONOSrun.R
R/dataImport.R
R/mRNAconversion.R
R/miRNAconversion.R
R/miRNAdownload.R
R/pathwayAnalysis.R
R/pathwayDownload.R
R/pathwayMeasures.R
R/pathwayToGraph.R
R/subExtractionLinear.R
R/subExtractionNonLinear.R
R/subRefinement.R
R/subScores.R
R/subStatistics.R
R/subVisualization.R
R/utilities.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/CHRONOS.R
inst/doc/CHRONOS.Rmd
inst/doc/CHRONOS.pdf
inst/extdata
inst/extdata/Downloads
inst/extdata/Downloads/KEGG
inst/extdata/Downloads/KEGG/hsa
inst/extdata/Downloads/KEGG/hsa/hsa04915.xml
inst/extdata/Downloads/KEGG/hsa/hsa04917.xml
inst/extdata/Downloads/KEGG/hsa/hsa04930.xml
inst/extdata/Downloads/KEGG/hsa/hsa05031.xml
inst/extdata/Downloads/mirbase
inst/extdata/Downloads/mirbase/miRNAmaps_cel.RData
inst/extdata/Downloads/mirbase/miRNAmaps_cfa.RData
inst/extdata/Downloads/mirbase/miRNAmaps_dme.RData
inst/extdata/Downloads/mirbase/miRNAmaps_dre.RData
inst/extdata/Downloads/mirbase/miRNAmaps_gga.RData
inst/extdata/Downloads/mirbase/miRNAmaps_hsa.RData
inst/extdata/Downloads/mirbase/miRNAmaps_mmu.RData
inst/extdata/Downloads/mirbase/miRNAmaps_oar.RData
inst/extdata/Downloads/mirbase/miRNAmaps_rno.RData
inst/extdata/Examples
inst/extdata/Examples/data.RData
inst/extdata/Examples/kgml
inst/extdata/Examples/kgml/hsa04915.xml
inst/extdata/Examples/kgml/hsa04917.xml
inst/extdata/Examples/kgml/hsa04930.xml
inst/extdata/Examples/kgml/hsa05031.xml
inst/extdata/User
inst/extdata/User/TarBase.xlsx
inst/extdata/User/interestingGenes.txt
inst/extdata/User/mRNAexpressions.txt
inst/extdata/User/miRNAexpressions.txt
inst/extdata/User/miRecords.xlsx
inst/java
inst/java/CHRONOS.jar
inst/unitTests
inst/unitTests/test_CHRONOSrun.R
inst/unitTests/test_pathwayToGraph.R
inst/unitTests/test_subExtractionLinear.R
inst/unitTests/test_subExtractionNonLinear.R
inst/unitTests/test_subRefinement.R
inst/unitTests/test_subVisualization.R
java
java/FileIO.java
java/Graph.java
java/LinearPaths.java
man
man/CHRONOSrun.Rd
man/convertMiRNANomenclature.Rd
man/convertNomenclature.Rd
man/createPathwayGraphs.Rd
man/downloadKEGGPathwayList.Rd
man/downloadMiRecords.Rd
man/downloadPathways.Rd
man/extractLinearSubpathways.Rd
man/extractNonLinearSubpathways.Rd
man/getEdgeTypes.Rd
man/importExpressions.Rd
man/pathwayMeasures.Rd
man/scoreSubpathways.Rd
man/subpathwayKEGGmap.Rd
man/subpathwayMiRNAs.Rd
man/visualizeResults.Rd
tests
tests/runTests.R
vignettes
vignettes/CHRONOS.Rmd
vignettes/figures
vignettes/figures/results.png
CHRONOS documentation built on May 20, 2017, 10:28 p.m.

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