API for JLP-BioInf/comradesOO
Analysis of RNA Crosslinking Data

Global functions
InputFiles	Man page
InputFiles,rnaCrosslinkDataSet-method	Man page
InputToGRanges	Man page Source code
addCluster	Source code
clusterGrangesList	Man page
clusterGrangesList,rnaCrosslinkDataSet-method	Man page
clusterGrangesList<-	Man page
clusterGrangesList<-,rnaCrosslinkDataSet-method	Man page
clusterNumbers	Man page
clusterNumbers,rnaCrosslinkDataSet-method	Man page
clusterTableFolded	Man page
clusterTableFolded,rnaCrosslinkDataSet-method	Man page
clusterTableList	Man page
clusterTableList,rnaCrosslinkDataSet-method	Man page
clusterTableList<-	Man page
clusterTableList<-,rnaCrosslinkDataSet-method	Man page
clusterrnaCrosslink	Man page
clusterrnaCrosslink,rnaCrosslinkDataSet-method	Man page
compareKnown	Man page
compareKnown,rnaCrosslinkDataSet-method	Man page
compareKnownStructures	Man page
compareKnownStructures,rnaCrosslinkDataSet-method	Man page
featureInfo	Man page
featureInfo,rnaCrosslinkDataSet-method	Man page
findBasePairsRNAcoFold2	Man page Source code
findBasePairsRNAfold	Man page Source code
findBasePairsRNAfold2	Man page Source code
foldrnaCrosslink	Man page
foldrnaCrosslink,rnaCrosslinkDataSet-method	Man page
getAdjacancyMat	Man page Source code
getClusterClusterShortRangeWhole	Man page Source code
getData	Man page
getData,rnaCrosslinkDataSet-method	Man page
getInteractions	Man page
getInteractions,rnaCrosslinkDataSet-method	Man page
getMatrices	Man page Source code
getReverseInteractions	Man page
getReverseInteractions,rnaCrosslinkDataSet-method	Man page
group	Man page
group,rnaCrosslinkDataSet-method	Man page
makeExamplernaCrosslinkDataSet	Man page Source code
matrixList	Man page
matrixList,rnaCrosslinkDataSet-method	Man page
matrixList<-	Man page
matrixList<-,rnaCrosslinkDataSet-method	Man page
plotClusterAgreement	Man page
plotClusterAgreement,rnaCrosslinkDataSet-method	Man page
plotClusterAgreementHeat	Man page
plotClusterAgreementHeat,rnaCrosslinkDataSet-method	Man page
plotCombinedMatrix	Man page
plotCombinedMatrix,rnaCrosslinkDataSet-method	Man page
plotComparisonArc	Man page
plotComparisonArc,rnaCrosslinkDataSet-method	Man page
plotEnsemblePCA	Man page
plotEnsemblePCA,rnaCrosslinkDataSet-method	Man page
plotInteractions	Man page
plotInteractions,rnaCrosslinkDataSet-method	Man page
plotInteractionsAverage	Man page
plotInteractionsAverage,rnaCrosslinkDataSet-method	Man page
plotMatrices	Man page
plotMatrices,rnaCrosslinkDataSet-method	Man page
plotMatricesAverage	Man page
plotMatricesAverage,rnaCrosslinkDataSet-method	Man page
plotStructure	Man page
plotStructure,rnaCrosslinkDataSet-method	Man page
printClustersFast	Man page Source code
readNumbers	Man page
readNumbers,rnaCrosslinkDataSet-method	Man page
rnaCrosslinkDataSet	Man page Source code
rnaCrosslinkDataSet-class	Man page
rnaCrosslinkOO	Man page
rnaCrosslinkQC	Man page Source code
rnaSize	Man page
rnaSize,rnaCrosslinkDataSet-method	Man page
rnas	Man page
rnas,rnaCrosslinkDataSet-method	Man page
sampleChimeras	Man page Source code
sampleNames	Man page
sampleNames,rnaCrosslinkDataSet-method	Man page
sampleTable	Man page
sampleTable,rnaCrosslinkDataSet-method	Man page
subsetInputList2	Man page Source code
swapInputs	Man page Source code
swapInputs2	Man page Source code
swapInputs3	Man page Source code
topInteracters	Man page
topInteracters,rnaCrosslinkDataSet-method	Man page
topInteractions	Man page
topInteractions,rnaCrosslinkDataSet-method	Man page
topTranscripts	Man page
topTranscripts,rnaCrosslinkDataSet-method	Man page
trimClusters	Man page
trimClusters,rnaCrosslinkDataSet-method	Man page