ballgown
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see ballgown.
Flexible, isoform-level differential expression analysis
Bioconductor version: 3.10
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("ballgown")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ballgown")
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("ballgown")| Flexible isoform-level differential expression analysis with Ballgown | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software, StatisticalMethod |
| Version | 2.18.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/alyssafrazee/ballgown/issues |
See More
| Suggests | testthat, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | RNASeqR |
| Suggests Me | polyester, variancePartition |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ballgown_2.18.0.tar.gz |
| Windows Binary | ballgown_2.18.0.zip |
| Mac OS X 10.11 (El Capitan) | ballgown_2.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ballgown |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ballgown |
| Bioc Package Browser | https://code.bioconductor.org/browse/ballgown/ |
| Package Short Url | https://bioconductor.org/packages/ballgown/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |