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Showing content from https://www.bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/ballgown.html below:

Bioconductor - ballgown (development version)

ballgown

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

Flexible, isoform-level differential expression analysis

Bioconductor version: Development (3.22)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.41.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 Package Archives

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

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