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:

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

To cite this package in a publication, start R and enter:

    citation("cummeRbund")

Documentation

PDF R Script CummeRbund User Guide
PDF Sample cummeRbund workflow
PDF   Reference Manual
Text   README
Text   NEWS

Details

biocViews Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, MultipleComparison, QualityControl, RNASeq, RNAseqData, Sequencing, Software, Visualization
Version 2.7.0
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 Downloads

Package Source cummeRbund_2.7.0.tar.gz
Windows Binary cummeRbund_2.7.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) cummeRbund_2.7.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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