clusterGrangesList |
clusterGrangesList |
clusterGrangesList-method |
clusterGrangesList |
clusterGrangesList<- |
clusterGrangesList<- |
clusterGrangesList<--method |
clusterGrangesList<- |
clusterNumbers |
clusterNumbers |
clusterNumbers-method |
clusterNumbers |
clusterrnaCrosslink |
clusterrnaCrosslink |
clusterrnaCrosslink-method |
clusterrnaCrosslink |
clusterTableFolded |
clusterTableFolded |
clusterTableFolded-method |
clusterTableFolded |
clusterTableList |
clusterTableList |
clusterTableList-method |
clusterTableList |
clusterTableList<- |
clusterTableList<- |
clusterTableList<--method |
clusterTableList<- |
compareKnown |
compareKnown |
compareKnown-method |
compareKnown |
compareKnownStructures |
compareKnownStructures |
compareKnownStructures-method |
compareKnownStructures |
featureInfo |
featureInfo |
featureInfo-method |
featureInfo |
findBasePairsRNAcoFold2 |
findBasePairsRNAcoFold2 |
findBasePairsRNAfold |
findBasePairsRNAfold |
findBasePairsRNAfold2 |
findBasePairsRNAfold2 |
foldrnaCrosslink |
foldrnaCrosslink |
foldrnaCrosslink-method |
foldrnaCrosslink |
getAdjacancyMat |
getAdjacancyMat |
getClusterClusterShortRangeWhole |
getClusterClusterShortRangeWhole |
getData |
getData |
getData-method |
getData |
getInteractions |
getInteractions |
getInteractions-method |
getInteractions |
getMatrices |
getMatrices |
getReverseInteractions |
getReverseInteractions |
getReverseInteractions-method |
getReverseInteractions |
group |
group |
group-method |
group |
InputFiles |
InputFiles |
InputFiles-method |
InputFiles |
InputToGRanges |
InputToGRanges |
makeExamplernaCrosslinkDataSet |
makeExamplernaCrosslinkDataSet |
matrixList |
matrixList |
matrixList-method |
matrixList |
matrixList<- |
matrixList |
matrixList<--method |
matrixList |
plotClusterAgreement |
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed |
plotClusterAgreement-method |
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed |
plotClusterAgreementHeat |
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed |
plotClusterAgreementHeat-method |
Plot a heatmap that plots the agreements between replicates after clusterrnaCrosslink has been performed |
plotCombinedMatrix |
Plots a contact map of two chosen samples for chosen stages in the analysis, with each chosen sample on separate halves of the contact map |
plotCombinedMatrix-method |
Plots a contact map of two chosen samples for chosen stages in the analysis, with each chosen sample on separate halves of the contact map |
plotComparisonArc |
plotComparisonArc |
plotComparisonArc-method |
plotComparisonArc |
plotEnsemblePCA |
plotEnsemblePCA |
plotEnsemblePCA-method |
plotEnsemblePCA |
plotInteractions |
Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interest |
plotInteractions-method |
Plots a contact map of interactions of each sample of an RNA (interactor) on the RNA of interest |
plotInteractionsAverage |
Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interest |
plotInteractionsAverage-method |
Plots a contact map of interactions of all samples of an RNA (interactor) on the RNA of interest |
plotMatrices |
Plots a number of contact maps to file of each sample for a stage in the analysis |
plotMatrices-method |
Plots a number of contact maps to file of each sample for a stage in the analysis |
plotMatricesAverage |
plotMatricesAverage |
plotMatricesAverage-method |
plotMatricesAverage |
plotStructure |
plotStructure |
plotStructure-method |
plotStructure |
printClustersFast |
printClustersFast |
readNumbers |
readNumbers |
readNumbers-method |
readNumbers |
rnaCrosslinkDataSet |
rnaCrosslinkDataSet |
rnaCrosslinkDataSet-class |
rnaCrosslinkDataSet |
rnaCrosslinkQC |
rnaCrosslinkQC |
rnas |
rnas |
rnas-method |
rnas |
rnaSize |
rnaSize |
rnaSize-method |
rnaSize |
sampleChimeras |
sampleChimeras |
sampleNames |
sampleNames |
sampleNames-method |
sampleNames |
sampleTable |
sampleTable |
sampleTable-method |
sampleTable |
subsetInputList2 |
subsetInputList2 |
swapInputs |
swapInputs |
swapInputs2 |
swapInputs2 |
swapInputs3 |
swapInputs3 |
topInteracters |
topInteracters |
topInteracters-method |
topInteracters |
topInteractions |
topInteractions |
topInteractions-method |
topInteractions |
topTranscripts |
topTranscripts |
topTranscripts-method |
topTranscripts |
trimClusters |
trimClusters |
trimClusters-method |
trimClusters |