To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

In most cases, you don't need to download the package archive at all.

cummeRbund

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

Bioconductor version: 2.13

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

Author: L. Goff, C. Trapnell, D. Kelley

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

Citation (from within R, enter citation("cummeRbund")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("cummeRbund")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cummeRbund")

 

PDF cuffData_schema.pdf
PDF R Script CummeRbund User Guide
PDF ENCODE_SCV.pdf
PDF R Script Sample cummeRbund workflow
PDF   Reference Manual
Text   README
Text   NEWS

Details

biocViews Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization
Version 2.4.1
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends R (>= 2.7.0), BiocGenerics(>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz
Imports methods, plyr, BiocGenerics
Suggests cluster, plyr
System Requirements
URL
Depends On Me spliceR
Imports Me
Suggests Me oneChannelGUI

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source cummeRbund_2.4.1.tar.gz
Windows Binary cummeRbund_2.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) cummeRbund_2.4.1.tgz
Browse/checkout source (username/password: readonly)
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