cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Bioconductor version: Release (3.19)
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 (version "4.4") 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 | 2.46.0 |
In Bioconductor since | BioC 2.9 (R-2.14) (13 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 | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | cummeRbund_2.46.0.tar.gz |
Windows Binary | cummeRbund_2.46.0.zip |
macOS Binary (x86_64) | cummeRbund_2.46.0.tgz |
macOS Binary (arm64) | cummeRbund_2.46.0.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 |