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cummeRbund (version 2.14.0)

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

Description

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

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Version

Version

2.14.0

License

Artistic-2.0

Maintainer

Last Published

February 15th, 2017

Functions in cummeRbund (2.14.0)

cummeRbund-package

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

Class "CuffSet"

CuffFeatureSet-class

Class "CuffFeatureSet"

Class "CuffDist"

Differential comparison data

Class "CuffData"

shannon.entropy

Shannon entropy

Get sample list from CuffData object

Get replicate sample list from CuffData object

Quality Control visualizations

CuffFeature-class

Class "CuffFeature"

Retrieve FPKM values

Mean count vs dispersion plot

expressionBarplot

Jensen-Shannon distance on rows from a pre-defined vector of probabilities

Class "CuffGene"

Dimensionality Reduction

Dimensionality reduction utilities

Transform a matrix into probabilities by columns

Retrieve run parameters and information from a CuffSet object

Retrieve count values (raw and normalized)

Expression Plot

repFpkm-methods

Retrieve FPKM values

CuffGeneSet-class

Class "CuffGeneSet"

Jensen-Shannon distance on columns

Density plot of CuffData

Exploratory Analysis

Methods for Exploratory Analysis in cummeRbund