cummeRbund-package {cummeRbund} | R Documentation

## cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~

### Description

Allows for persistent storage, access, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. ~~ A concise (1-5 lines) description of the package ~~

### Details

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)

~~ An overview of how to use the package, including the most important ~~ ~~ functions ~~

### Author(s)

L. Goff, C. Trapnell

Maintainer: Loyal A. Goff <lgoff@csail.mit.edu>

### References

~~ Literature or other references for background information ~~

[Package cummeRbund version 2.30.0 Index]