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ballgown

Flexible, isoform-level differential expression analysis


Bioconductor version: Release (3.18)

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 2.34.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
URL
Bug Reports https://github.com/alyssafrazee/ballgown/issues
See More
Suggests testthat, knitr, markdown
Linking To
Enhances
Depends On Me VaSP
Imports Me
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_2.34.0.tar.gz
Windows Binary ballgown_2.34.0.zip
macOS Binary (x86_64) ballgown_2.34.0.tgz
macOS Binary (arm64) ballgown_2.34.0.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