cummeRbund

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see cummeRbund.

All versions

3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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

Bioconductor version: Release (3.23)

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")):

L. Goff, C. Trapnell, D. Kelley. cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data. doi:10.18129/B9.bioc.cummeRbund, R package version 2.54.0, https://bioconductor.org/packages/cummeRbund.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization
Version	2.54.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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
URL

Suggests	cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/cummeRbund
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cummeRbund
Package Short Url	https://bioconductor.org/packages/cummeRbund/
Package Downloads Report	Download Stats