cummeRbund

DOI: 10.18129/B9.bioc.cummeRbund    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see cummeRbund.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF	R Script	CummeRbund User Guide
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	2.26.0
In Bioconductor since	BioC 2.9 (R-2.14) (8 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
LinkingTo
Suggests	cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	meshr
Suggests Me	IsoformSwitchAnalyzeR
Links To Me
Build Report

Package Archives

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

Source Package	cummeRbund_2.26.0.tar.gz
Windows Binary	cummeRbund_2.26.0.zip
Mac OS X 10.11 (El Capitan)	cummeRbund_2.26.0.tgz
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