ballgown

DOI: 10.18129/B9.bioc.ballgown    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see ballgown.

Flexible, isoform-level differential expression analysis

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DifferentialExpression, ImmunoOncology, Preprocessing, RNASeq, Software, StatisticalMethod
Version	2.24.0
In Bioconductor since	BioC 3.0 (R-3.1) (7 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
LinkingTo
Suggests	testthat, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/alyssafrazee/ballgown/issues
Depends On Me	VaSP
Imports Me	RNASeqR
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_2.24.0.tar.gz
Windows Binary	ballgown_2.24.0.zip
macOS 10.13 (High Sierra)	ballgown_2.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ballgown
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ballgown
Package Short Url	https://bioconductor.org/packages/ballgown/
Package Downloads Report	Download Stats