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

This is the development version of cummeRbund; for the stable release version, see cummeRbund.

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

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

Installation

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 R Script CummeRbund User Guide
PDF 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 2.7.2
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, Biobase
Suggests cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
System Requirements
URL
Depends On Me meshr, spliceR
Imports Me
Suggests Me oneChannelGUI

Package Archives

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

Package Source cummeRbund_2.7.2.tar.gz
Windows Binary cummeRbund_2.7.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) cummeRbund_2.7.2.tgz
Mac OS X 10.9 (Mavericks) cummeRbund_2.7.2.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center