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Bioconductor - DEXSeq (development version)

DEXSeq

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

Inference of differential exon usage in RNA-Seq

Bioconductor version: Development (3.22)

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

Author: Simon Anders <sanders at fs.tum.de> and Alejandro Reyes <alejandro.reyes.ds at gmail.com>

Maintainer: Alejandro Reyes <alejandro.reyes.ds at gmail.com>

Citation (from within R, enter citation("DEXSeq")): 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("DEXSeq")

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("DEXSeq")
Inferring differential exon usage in RNA-Seq data with the DEXSeq package HTML R Script Reference Manual PDF NEWS Text Details biocViews AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization Version 1.55.1 In Bioconductor since BioC 2.9 (R-2.14) (13.5 years) License GPL (>= 3) Depends BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors(>= 0.23.18) Imports BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter System Requirements URL See More Suggests GenomeInfoDb, GenomicFeatures, txdbmaker, pasilla(>= 0.2.22), BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi Linking To Enhances Depends On Me IsoformSwitchAnalyzeR, pasilla, rnaseqDTU Imports Me diffUTR, IntEREst, pairedGSEA Suggests Me bambu, GenomicRanges, satuRn, stageR, subSeq, BioPlex Links To Me Build Report Build Report Package Archives

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

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