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

Global functions
.Sys.which2 Source code
.betweennessCentrality Source code
.bridgeness Source code
.buildDirectories Source code
.cleanDirectories Source code
.collapseSubpaths Source code
.createDirectories Source code
.createExcelOutputMulti Source code
.createExcelOutputSingle Source code
.createMirnaLexicon Source code
.degree Source code
.doSafeParallel Source code
.downloadPathways Source code
.evaluateSubpaths Source code
.extractLinearSubpathways Source code
.extractNonLinearSubpathways Source code
.filterExpressions Source code
.filterLinearSubpaths Source code
.filterMiScores Source code
.filterRecords Source code
.filterSubScore Source code
.getEdgeScores Source code
.getFilters Source code
.getMeasures Source code
.getMiRNAtargetsUrl Source code
.getMiRecordsData Source code
.getMiRecordsMiRNAs Source code
.getMiScores Source code
.getProcessedData Source code
.getStatistics Source code
.getValMiRecordsTargets Source code
.getValTarbaseTargets Source code
.indexSubpaths Source code
.mRNAconversion Source code
.markov Source code
.nlSubpaths Source code
.onAttach Source code
.onLoad Source code
.onUnload Source code
.scoreSubpaths Source code
.scoreSubpathways Source code
.uniquifySubpaths Source code
CHRONOSrun Man page Source code
checkFile Source code
cleanSubpath Source code
convertMiRNANomenclature Man page Source code
convertNomenclature Man page Source code
createKEGGLink Source code
createKEGGLinks Source code
createPathwayGraphs Man page Source code
createScoreFile Source code
doCirclize Source code
downloadKEGGPathwayList Man page Source code
downloadMiRecords Man page Source code
downloadPathway Source code
downloadPathways Man page 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
extractNonLinearSubpathways Man page Source code
fillMatrixList Source code
filterLinearSubpaths Source code
filterMatrix Source code
fk Source code
fullCollapse Source code
getDoubleEdges Source code
getEdgeTypes Man page Source code
getLengths Source code
getLinearPairs Source code
getLinearSubpath Source code
getPathwayType Source code
getSplittingFactor Source code
getSubpathwayGenes Source code
idxToMat Source code
importExpressions Man page Source code
importGeneExpressions Source code
importMiRNAExpressions Source code
importMiRNAFile Source code
indexSubpath Source code
matrixToFile Source code
matrixToLexicon Source code
matrixToList Source code
metabolicPathwayToGraph Source code
miRNAsubScoring Source code
mirParser Source code
mirRenamer Source code
nonMetabolicPathwayToGraph Source code
normalize Source code
optimalLengths Source code
pathwayMeasures Man page Source code
removeCompoundsMetabolicGraph Source code
removeCompoundsNonMetabolicGraph Source code
saveMiRNAFile Source code
scoreFCI Source code
scoreSubpathways Man page Source code
scoreTVI Source code
splitWork Source code
subpathExpansion Source code
subpathwayKEGGmap Man page Source code
subpathwayMiRNAs Man page Source code
unlistToMatrix Source code
visualizeResults Man page Source code
CHRONOS documentation built on Oct. 31, 2019, 2:16 a.m.