ballgown

DOI: 10.18129/B9.bioc.ballgown    

Flexible, isoform-level differential expression analysis

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ballgown")

Documentation

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

Details

biocViews	DifferentialExpression, Preprocessing, RNASeq, Software, StatisticalMethod
Version	2.10.0
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 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
Imports Me
Suggests Me	polyester, variancePartition
Build Report

Package Archives

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

Source Package	ballgown_2.10.0.tar.gz
Windows Binary	ballgown_2.10.0.zip
Mac OS X 10.11 (El Capitan)	ballgown_2.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ballgown
Package Short Url	http://bioconductor.org/packages/ballgown/
Package Downloads Report	Download Stats