DEXSeq: Inference of differential exon usage in RNA-Seq

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
AuthorSimon Anders <sanders@fs.tum.de> and Alejandro Reyes <alejandro.reyes@embl.de>
Bioconductor views AlternativeSplicing DifferentialExpression DifferentialSplicing GeneExpression RNASeq Sequencing Visualization
Date of publicationNone
MaintainerAlejandro Reyes <alejandro.reyes@embl.de>
LicenseGPL (>= 3)
Version1.20.2

View on Bioconductor

Functions

colData<-,DEXSeqDataSet,DataFrame-method Man page
counts Man page
counts,DEXSeqResults-method Man page
DEXSeq Man page
DEXSeqDataSet Man page
[,DEXSeqDataSet,ANY,ANY,ANY-method Man page
[,DEXSeqDataSet,ANY,ANY-method Man page
[,DEXSeqDataSet,ANY-method Man page
DEXSeqDataSet-class Man page
DEXSeqDataSetFromHTSeq Man page
DEXSeqDataSetFromSE Man page
[,DEXSeqDataSet-method Man page
$<-,DEXSeqDataSet-method Man page
DEXSeq-defunct Man page
DEXSeqHTML Man page
DEXSeqResults Man page
DEXSeqResults-class Man page
estimateDispersions Man page
estimateDispersions,DEXSeqDataSet-method Man page
estimateExonFoldChanges Man page
estimateSizeFactors Man page
estimateSizeFactors,DEXSeqDataSet-method Man page
exonIDs Man page
exonIDs<- Man page
featureCounts Man page
featureIDs Man page
featureIDs<- Man page
findOverlaps Man page
findOverlaps,DEXSeqResults,GenomicRanges-method Man page
findOverlaps-methods Man page
geneIDs Man page
geneIDs<- Man page
groupIDs Man page
groupIDs<- Man page
perGeneQValue Man page
plotDEXSeq Man page
plotDispEsts Man page
plotDispEsts,DEXSeqDataSet-method Man page
plotMA Man page
plotMA,DEXSeqDataSet-method Man page
plotMA,DEXSeqResults-method Man page
plotMA-methods Man page
sampleAnnotation Man page
subsetByOverlaps Man page
subsetByOverlaps,DEXSeqResults,GenomicRanges-method Man page
subsetByOverlaps-methods Man page
testForDEU Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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