cummeRbund

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

Bioconductor version: 3.23 · Package version: 2.54.0

Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

Installation

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

BiocManager::install("cummeRbund")

Details

Maintainer	Loyal A. Goff <lgoff@csail.mit.edu>
Author	L. Goff, C. Trapnell, D. Kelley
License	Artistic-2.0
Status	Deprecated
Downloads rank	493
Source branch	RELEASE_3_23
biocViews	Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization

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Source package

Dependencies

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