| Package: |
| cummeRbund |
| Version: |
| 0.1.3 |
| Suggests: |
| Depends: |
| R (>= 2.7.0), RSQLite, reshape2, ggplot2, methods |
| License: |
| MIT License |
| Collate: |
| AllGenerics.R AllClasses.R database-setup.R methods-CuffSet.R methods-CuffData.R methods-CuffDist.R methods-CuffGeneSet.R methods-CuffFeatureSet.R methods-CuffGene.R methods-CuffFeature.R tools.R |
| LazyLoad: |
| yes |
| biocViews: |
| HighThroughputSequencing, HighThroughputSequencingData, RNAseq, RNAseqData, GeneExpression, DifferentialExpression, Infrastructure, DataImport, DataRepresentation, Visualization, Bioinformatics, Clustering, MultipleComparisons, QualityControl |
| Packaged: |
| 2011-08-05 18:03:50 UTC; lgoff |
| Built: |
| R 2.12.1; ; 2011-08-05 18:03:57 UTC; unix |
Index:
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"
JSdist Jensen-Shannon distance on columns
addFeatures addFeatures
addFeatures-methods ~~ Methods for Function addFeatures in Package
'cummeRbund' ~~
createDB createDB
csBoxplot csBoxplot
csBoxplot-methods ~~ Methods for Function csBoxplot in Package
'cummeRbund' ~~
csDensity Density plot of CuffData
csDensity-methods ~~ Methods for Function csDensity in Package
'cummeRbund' ~~
csHeatmap csHeatmap
csHeatmap-methods ~~ Methods for Function csHeatmap in Package
'cummeRbund' ~~
csScatter Scatter Plot
csScatter-methods ~~ Methods for Function csScatter in Package
'cummeRbund' ~~
csVolcano Volcano Plot
csVolcano-methods ~~ Methods for Function csVolcano in Package
'cummeRbund' ~~
cummeRbund-package cummeRbund: The finishing touch on your Tuxedo
workflow. Analysis, manipulation, and
visualization of Cufflinks HTS data.
diffData Differential comparison data
diffData-methods ~~ Methods for Function diffData in Package
'cummeRbund' ~~
dim-methods ~~ Methods for Function dim in Package 'base'
~~
expressionBarplot Barplot
expressionBarplot-methods
~~ Methods for Function expressionBarplot in
Package 'cummeRbund' ~~
expressionPlot Expression Plot
expressionPlot-methods
~~ Methods for Function expressionPlot in
Package 'cummeRbund' ~~
featureNames Feature names
featureNames-methods ~~ Methods for Function featureNames in Package
'cummeRbund' ~~
features Features
features-methods ~~ Methods for Function features in Package
'cummeRbund' ~~
fpkm Retrieve FPKM values
fpkm-methods ~~ Methods for Function fpkm in Package
'cummeRbund' ~~
fpkmMatrix Retrieve FPKM values as matrix
fpkmMatrix-methods ~~ Methods for Function fpkmMatrix in Package
'cummeRbund' ~~
getGene getGene
getGene-methods ~~ Methods for Function getGene in Package
'cummeRbund' ~~
getGenes getGenes
getGenes-methods ~~ Methods for Function getGenes in Package
'cummeRbund' ~~
getLevels getLevels
getLevels-methods ~~ Methods for Function getLevels in Package
'cummeRbund' ~~
length-methods ~~ Methods for Function length in Package
'base' ~~
makeprobs Transform a matrix into probabilities by
columns
readCufflinks readCufflinks
samples Get sample list from CuffData object
samples-methods ~~ Methods for Function samples in Package
'cummeRbund' ~~
shannon.entropy Shannon entropy
Further information is available in the following vignettes:
cummeRbund-manual |
| An R package for visualization and analysis of Cufflinks high-throughput sequencing data (source, pdf) |