cummeRbund
This package is for version 3.10 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: 3.10
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("cummeRbund")):
Installation
To install this package, start R (version "3.6") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("cummeRbund")| CummeRbund User Guide | R Script | |
| Sample cummeRbund workflow | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | Bioinformatics, Clustering, DataImport, DataRepresentation, DifferentialExpression, GeneExpression, HighThroughputSequencing, HighThroughputSequencingData, Infrastructure, MultipleComparisons, QualityControl, RNAseq, RNAseqData, Software, Visualization |
| Version | 2.28.0 |
| 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 | |
| URL |
See More
| Suggests | cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | meshr |
| Suggests Me | IsoformSwitchAnalyzeR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cummeRbund_2.28.0.tar.gz |
| Windows Binary | cummeRbund_2.28.0.zip |
| Mac OS X 10.11 (El Capitan) | cummeRbund_2.28.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |