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ballgown

Flexible, isoform-level differential expression analysis

Bioconductor version: Release (3.17)

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 (version "4.3") 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 PDF
NEWS Text

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software, StatisticalMethod
Version 2.32.0
In Bioconductor since BioC 3.0 (R-3.1) (9 years)
License Artistic-2.0
Depends R (>= 3.5.0), 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
Linking To
Suggests testthat, knitr, markdown
System Requirements
Enhances
URL
Bug Reports https://github.com/alyssafrazee/ballgown/issues
See More
Depends On Me VaSP
Imports Me
Suggests Me polyester, variancePartition
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ballgown_2.32.0.tar.gz
Windows Binary ballgown_2.32.0.zip
macOS Binary (x86_64) ballgown_2.32.0.tgz
macOS Binary (arm64) ballgown_2.32.0.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