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" |