Man pages for cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
| addFeatures | addFeatures |
| count | Retrieve count values (raw and normalized) |
| countMatrix | countMatrix |
| csBoxplot | csBoxplot |
| csCluster | csCluster |
| csClusterPlot | csClusterPlot |
| csDendro | csDendro |
| csDensity | Density plot of CuffData |
| csDistHeat | csDistHeat |
| csHeatmap | csHeatmap |
| csScatter | Scatter Plot |
| csSpecificity | csSpecificity |
| csVolcano | 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-package | cummeRbund: The finishing touch on your Tuxedo workflow.... |
| diffData | Differential comparison data |
| dimensionality | Dimensionality reduction utilities |
| dispersionPlot | Mean count vs dispersion plot |
| distValues | distValues |
| exploratory | Methods for Exploratory Analysis in cummeRbund |
| expressionBarplot | Barplot |
| expressionPlot | Expression Plot |
| featureNames | Feature names |
| features | Features |
| findGene | findGene |
| findSimilar | findSimilar |
| fpkm | Retrieve FPKM values |
| fpkmMatrix | fpkmMatrix |
| getFeatures | getFeatures |
| getGene | getGene |
| getGeneId | getGene |
| getGenes | getGenes |
| getLevels | getLevels |
| getRepLevels | getRepLevels |
| getSig | getSig |
| getSigTable | getSigTable |
| JSdist | Jensen-Shannon distance on columns |
| JSdistFromP | Jensen-Shannon distance on rows from a pre-defined vector of... |
| JSdistVec | JSdistVec |
| makeprobs | Transform a matrix into probabilities by columns |
| makeprobsvec | makeprobsvec |
| MAplot | MAplot |
| PINK1 | PINK1 |
| QCplots | Quality Control visualizations |
| readCufflinks | readCufflinks |
| repFpkm | Retrieve FPKM values |
| replicates | Get replicate sample list from CuffData object |
| runInfo | Retrieve run parameters and information from a CuffSet object |
| sampleGeneSet | sampleGeneSet |
| sampleIDs | sampleIDs |
| samples | Get sample list from CuffData object |
| shannon.entropy | Shannon entropy |
| sigMatrix | sigMatrix |
