cummeRbund

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

Bioconductor version: Release (2.12)

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		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	2.2.0
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
Imports Me
Suggests Me	oneChannelGUI

Package Downloads

Package Source	cummeRbund_2.2.0.tar.gz
Windows Binary	cummeRbund_2.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	cummeRbund_2.2.0.tgz
Package Downloads Report	Download Stats

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