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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ballgown")
In most cases, you don't need to download the package archive at all.
ballgown
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ballgown.
Flexible, isoform-level differential expression analysis
Bioconductor version: 3.3
Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
Author: Jack Fu [aut], Alyssa C. Frazee [aut, cre], Leonardo Collado-Torres [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Jack Fu <jmfu at jhsph.edu>
Citation (from within R,
enter citation("ballgown")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ballgown")
Documentation
| HTML | R Script | Flexible isoform-level differential expression analysis with Ballgown |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, Preprocessing, RNASeq, Software, StatisticalMethod |
| Version | 2.4.3 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1.1), methods |
| Imports | GenomicRanges(>= 1.17.25), IRanges(>= 1.99.22), S4Vectors(>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer(>= 1.29.25), Biobase(>= 2.25.0), GenomeInfoDb |
| LinkingTo | |
| Suggests | testthat, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| BugReports | https://github.com/alyssafrazee/ballgown/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | polyester, variancePartition |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ballgown_2.4.3.tar.gz |
| Windows Binary | ballgown_2.4.3.zip |
| Mac OS X 10.9 (Mavericks) | ballgown_2.4.3.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ballgown/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/ballgown/ |
| Package Downloads Report | Download Stats |
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