Registration Open for Bioc2024 July 24-26


This is the development version of ballgown; for the stable release version, see ballgown.

Flexible, isoform-level differential expression analysis

Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("ballgown")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Flexible isoform-level differential expression analysis with Ballgown HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software, StatisticalMethod
Version 2.37.0
In Bioconductor since BioC 3.0 (R-3.1) (10 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
System Requirements
Bug Reports
See More
Suggests testthat, knitr, markdown
Linking To
Depends On Me VaSP
Imports Me
Suggests Me variancePartition
Links To Me
Build Report Build Report

Package Archives

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

Source Package ballgown_2.37.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) ballgown_2.37.0.tgz
macOS Binary (arm64) ballgown_2.37.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats