DOI: 10.18129/B9.bioc.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 (3.17)

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>

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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



PDF R Script CummeRbund User Guide
PDF R Script Sample cummeRbund workflow
PDF   Reference Manual


biocViews Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization
Version 2.41.0
In Bioconductor since BioC 2.9 (R-2.14) (11 years)
License Artistic-2.0
Depends R (>= 2.7.0), BiocGenerics(>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz
Imports methods, plyr, BiocGenerics, S4Vectors(>= 0.9.25), Biobase
Suggests cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package cummeRbund_2.41.0.tar.gz
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