cummeRbund-package: cummeRbund: The finishing touch on your Tuxedo workflow....

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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 <[e-mail]>

References

~~ Literature or other references for background information ~~

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.