ballgown

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see ballgown.

Flexible, isoform-level differential expression analysis

Bioconductor version: 3.16

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 "4.2") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software, StatisticalMethod

Version 2.30.0

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

Suggests testthat, knitr, markdown

Linking To

Enhances

Depends On Me VaSP

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_2.30.0.tar.gz

Windows Binary ballgown_2.30.0.zip

macOS Binary (x86_64) ballgown_2.30.0.tgz

macOS Binary (arm64) ballgown_2.30.0.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 3.16 Source Archive