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cummeRbund

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


Bioconductor version: Release (3.18)

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 (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cummeRbund")

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

Documentation

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

browseVignettes("cummeRbund")
CummeRbund User Guide PDF R Script
Sample cummeRbund workflow PDF R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization
Version 2.44.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
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Suggests cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
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Depends On Me
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Package Archives

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

Source Package cummeRbund_2.44.0.tar.gz
Windows Binary cummeRbund_2.44.0.zip
macOS Binary (x86_64) cummeRbund_2.44.0.tgz
macOS Binary (arm64) cummeRbund_2.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/cummeRbund
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cummeRbund
Bioc Package Browser https://code.bioconductor.org/browse/cummeRbund/
Package Short Url https://bioconductor.org/packages/cummeRbund/
Package Downloads Report Download Stats