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A C D E F G I J L M P R S T V misc
| cummeRbund-package | cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~ |
| addFeatures | addFeatures |
| addFeatures-method | addFeatures |
| annotation | Class "CuffFeatureSet" |
| annotation-method | Class "CuffData" |
| annotation-method | Class "CuffFeature" |
| annotation-method | Class "CuffFeatureSet" |
| CDS | Class "CuffSet" |
| CDS-method | Class "CuffGene" |
| CDS-method | Class "CuffGeneSet" |
| CDS-method | Class "CuffSet" |
| conditions | Class "CuffSet" |
| conditions-method | Class "CuffSet" |
| count | Retrieve count values (raw and normalized) |
| count-method | Retrieve count values (raw and normalized) |
| count-methods | Retrieve count values (raw and normalized) |
| countMatrix | countMatrix |
| countMatrix-method | countMatrix |
| csBoxplot | csBoxplot |
| csBoxplot-method | csBoxplot |
| csCluster | csCluster |
| csCluster-method | csCluster |
| csClusterPlot | csClusterPlot |
| csDendro | csDendro |
| csDendro-method | csDendro |
| csDensity | Density plot of CuffData |
| csDensity-method | Density plot of CuffData |
| csDistHeat | csDistHeat |
| csDistHeat-method | csDistHeat |
| csFoldChangeHeatmap | csHeatmap |
| csFoldChangeHeatmap-method | csHeatmap |
| csHeatmap | csHeatmap |
| csHeatmap-method | csHeatmap |
| csNMF | Methods for Exploratory Analysis in cummeRbund |
| csNMF-method | Methods for Exploratory Analysis in cummeRbund |
| csPie | Class "CuffGene" |
| csPie-method | Class "CuffGene" |
| csScatter | Scatter Plot |
| csScatter-method | Scatter Plot |
| csScatterMatrix | Scatter Plot |
| csScatterMatrix-method | Scatter Plot |
| csSpecificity | csSpecificity |
| csSpecificity-method | csSpecificity |
| csVolcano | Volcano Plot |
| csVolcano-method | Volcano Plot |
| csVolcanoMatrix | Volcano Plot |
| csVolcanoMatrix-method | Volcano Plot |
| CuffData-class | Class "CuffData" |
| CuffDist-class | Class "CuffDist" |
| CuffFeature-class | Class "CuffFeature" |
| CuffFeatureSet-class | Class "CuffFeatureSet" |
| CuffGene-class | Class "CuffGene" |
| CuffGeneSet-class | Class "CuffGeneSet" |
| CuffSet-class | Class "CuffSet" |
| cummeRbund | cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~ |
| DB | Class "CuffSet" |
| DB-method | Class "CuffData" |
| DB-method | Class "CuffDist" |
| DB-method | Class "CuffSet" |
| diffData | Differential comparison data |
| diffData-method | Class "CuffFeature" |
| diffData-method | Class "CuffFeatureSet" |
| diffData-method | Differential comparison data |
| diffTable | Differential comparison data |
| diffTable-method | Differential comparison data |
| dim-method | Class "CuffData" |
| dim-method | Class "CuffDist" |
| dispersionPlot | Mean count vs dispersion plot |
| dispersionPlot-method | Mean count vs dispersion plot |
| distValues | distValues |
| distValues-method | distValues |
| expressionBarplot | Barplot |
| expressionBarplot-method | Barplot |
| expressionPlot | Expression Plot |
| expressionPlot-method | Expression Plot |
| featureNames-method | Class "CuffFeatureSet" |
| featureNames-method | Feature names |
| features | Features |
| features-method | Class "CuffFeatureSet" |
| features-method | Features |
| findGene | findGene |
| findGene-method | findGene |
| findSimilar | findSimilar |
| findSimilar-method | findSimilar |
| fpkm | Retrieve FPKM values |
| fpkm-method | Retrieve FPKM values |
| fpkm-methods | Retrieve FPKM values |
| fpkmMatrix | fpkmMatrix |
| fpkmMatrix-method | Class "CuffFeature" |
| fpkmMatrix-method | fpkmMatrix |
| fpkmSCVPlot | Quality Control visualizations |
| fpkmSCVPlot-method | Quality Control visualizations |
| genePlot | Class "CuffGene" |
| genePlot-method | Class "CuffGene" |
| genes | Class "CuffSet" |
| genes-method | Class "CuffGene" |
| genes-method | Class "CuffGeneSet" |
| genes-method | Class "CuffSet" |
| getFeatures | getFeatures |
| getFeatures-method | Class "CuffData" |
| getFeatures-method | getFeatures |
| getGene | getGene |
| getGene-method | getGene |
| getGeneId | getGene |
| getGeneId-method | getGene |
| getGenes | getGenes |
| getGenes-method | getGenes |
| getLevels | getLevels |
| getLevels-method | getLevels |
| getRepLevels | getRepLevels |
| getRepLevels-method | getRepLevels |
| getSig | getSig |
| getSig-method | getSig |
| getSigTable | getSigTable |
| getSigTable-method | getSigTable |
| isoforms | Class "CuffSet" |
| isoforms-method | Class "CuffGene" |
| isoforms-method | Class "CuffGeneSet" |
| isoforms-method | Class "CuffSet" |
| JSdist | Jensen-Shannon distance on columns |
| JSdistFromP | Jensen-Shannon distance on rows from a pre-defined vector of probabilities |
| JSdistVec | JSdistVec |
| length-method | Class "CuffFeature" |
| length-method | Class "CuffFeatureSet" |
| length-method | Class "CuffGene" |
| makeGeneRegionTrack | Class "CuffGene" |
| makeGeneRegionTrack-method | Class "CuffGene" |
| makeprobs | Transform a matrix into probabilities by columns |
| makeprobsvec | makeprobsvec |
| makeRnk | Class "CuffData" |
| makeRnk-method | Class "CuffData" |
| MAplot | MAplot |
| MAplot-method | MAplot |
| MDSplot | Dimensionality reduction utilities |
| MDSplot-method | Dimensionality reduction utilities |
| PCAplot | Dimensionality reduction utilities |
| PCAplot-method | Dimensionality reduction utilities |
| PINK1 | PINK1 |
| promoters | Class "CuffSet" |
| promoters-method | Class "CuffGene" |
| promoters-method | Class "CuffGeneSet" |
| promoters-method | Class "CuffSet" |
| readCufflinks | readCufflinks |
| relCDS | Class "CuffSet" |
| relCDS-method | Class "CuffGene" |
| relCDS-method | Class "CuffGeneSet" |
| relCDS-method | Class "CuffSet" |
| repCountMatrix | countMatrix |
| repCountMatrix-method | countMatrix |
| repFpkm | Retrieve FPKM values |
| repFpkm-method | Retrieve FPKM values |
| repFpkm-methods | Retrieve FPKM values |
| repFpkmMatrix | fpkmMatrix |
| repFpkmMatrix-method | fpkmMatrix |
| replicates | Get replicate sample list from CuffData object |
| replicates-method | Get replicate sample list from CuffData object |
| runInfo | Retrieve run parameters and information from a CuffSet object |
| runInfo-method | Retrieve run parameters and information from a CuffSet object |
| sampleGeneSet | sampleGeneSet |
| sampleIDs | sampleIDs |
| samples | Get sample list from CuffData object |
| samples-method | Class "CuffDist" |
| samples-method | Class "CuffFeature" |
| samples-method | Class "CuffFeatureSet" |
| samples-method | Get sample list from CuffData object |
| shannon.entropy | Shannon entropy |
| sigMatrix | sigMatrix |
| sigMatrix-method | sigMatrix |
| splicing | Class "CuffSet" |
| splicing-method | Class "CuffGene" |
| splicing-method | Class "CuffGeneSet" |
| splicing-method | Class "CuffSet" |
| TSS | Class "CuffSet" |
| TSS-method | Class "CuffGene" |
| TSS-method | Class "CuffGeneSet" |
| TSS-method | Class "CuffSet" |
| varModel | Class "CuffSet" |
| varModel-method | Class "CuffSet" |
| [-method | Class "CuffSet" |