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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
In most cases, you don't need to download the package archive at all.
cummeRbund
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Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Bioconductor version: Release (3.1)
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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("cummeRbund")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cummeRbund")
| R Script | CummeRbund User Guide | |
| Sample cummeRbund workflow | ||
| Reference Manual | ||
| Text | README | |
| Text | NEWS |
Details
| biocViews | Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization |
| Version | 2.10.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.7.0), BiocGenerics(>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz |
| Imports | methods, plyr, BiocGenerics, Biobase |
| LinkingTo | |
| Suggests | cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | meshr, spliceR |
| Imports Me | |
| Suggests Me | oneChannelGUI |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | cummeRbund_2.10.0.tar.gz |
| Windows Binary | cummeRbund_2.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | cummeRbund_2.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | cummeRbund_2.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/cummeRbund/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/cummeRbund/ |
| Package Downloads Report | Download Stats |
Documentation »
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