DEXSeq: Inference of differential exon usage in RNA-Seq
Version 1.22.0

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.

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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)
Version1.22.0
URL
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DEXSeq")

Man pages

accessors: Accessor functions for DEXSeqDataSet details
counts: Accessors for the 'counts' slot of a DEXSeqResults object.
DEXSeq: Performs the differential exon usage test in a single command
DEXSeqDataSet: DEXSeqDataSet object and constructors
DEXSeq-defunct: This functions are deprecated and will become defunct.
DEXSeqHTML: DEXSeq HTML report writer
DEXSeqResults: DEXSeqResults object
estimateDispersions: Estimate the dispersions for a DEXSeqDataSet
estimateExonFoldChanges: Estimates exon usage coefficients from the fitted terms of...
estimateSizeFactors: Estimate the size factors for a DEXSeqDataSet
methods-gr: Methods from GRanges overlaps for the DEXSeq object
otherMethods: Subset and replacements of DEXSeqDataSet slots
perGeneQValue: Summarize per-exon p-values into per-gene q-values.
plotDEXSeq: Visualization of the per gene DEXSeq results.
plotDispEsts: Plot dispersion estimates
plotMA: Generate an MA plot
testForDEU: Test for Differential Exon Usage.

Functions

$<-,DEXSeqDataSet-method Man page
DEXSeq Man page Source code
DEXSeq-defunct Man page
DEXSeqDataSet Man page Source code
DEXSeqDataSet-class Man page
DEXSeqDataSetFromHTSeq Man page Source code
DEXSeqDataSetFromSE Man page Source code
DEXSeqHTML Man page Source code
DEXSeqResults Man page Source code
DEXSeqResults-class Man page
[,DEXSeqDataSet,ANY,ANY,ANY-method Man page
[,DEXSeqDataSet,ANY,ANY-method Man page
[,DEXSeqDataSet,ANY-method Man page
[,DEXSeqDataSet-method Man page
apply2 Source code
arrangeCoefs Source code
balanceExons Source code
colData<-,DEXSeqDataSet,DataFrame-method Man page
counts Man page
counts,DEXSeqResults-method Man page
counts.DEXSeqResults Source code
drawGene Source code
drawPlot Source code
estimateDispersions Man page
estimateDispersions,DEXSeqDataSet-method Man page
estimateDispersions.DEXSeqDataSet Source code
estimateExonFoldChanges Man page Source code
estimateSizeFactors Man page
estimateSizeFactors,DEXSeqDataSet-method Man page
estimateSizeFactors.DEXSeqDataSet Source code
exonIDs Man page Source code
exonIDs<- Man page
featureCounts Man page Source code
featureIDs Man page Source code
featureIDs<- Man page
findOverlaps Man page
findOverlaps,DEXSeqResults,GenomicRanges-method Man page
findOverlaps-methods Man page
findOverlaps.DEXSeqResults Source code
fitAndArrangeCoefs Source code
geneIDs Man page Source code
geneIDs<- Man page
getEffectsForExonsSM Source code
getEffectsForGene Source code
getEffectsForGeneBM Source code
getEffectsForPlotting Source code
groupIDs Man page Source code
groupIDs<- Man page
makeBigModelFrame Source code
makePlotPage Source code
makevstaxis Source code
modelFrameSM Source code
perGeneQValue Man page Source code
perGeneQValueBySimulation Source code
perGeneQValueExact Source code
plotDEXSeq Man page Source code
plotDispEsts Man page
plotDispEsts,DEXSeqDataSet-method Man page
plotDispEsts.DEXSeqDataSet Source code
plotMA Man page
plotMA,DEXSeqDataSet-method Man page
plotMA,DEXSeqResults-method Man page
plotMA-methods Man page
plotMA.DEXSeqDataSet Source code
plotMA.DEXSeqResults Source code
rmDepCols Source code
sampleAnnotation Man page Source code
show.DEXSeqResults Source code
subsetByOverlaps Man page
subsetByOverlaps,DEXSeqResults,GenomicRanges-method Man page
subsetByOverlaps-methods Man page
subsetByOverlaps.DEXSeqResults Source code
testForDEU Man page Source code
vst Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/classes.R
R/coef_handling.R
R/core.R
R/deprecatedFunctions.R
R/htmlReports.R
R/methods.R
R/perGeneQValue.R
R/visualization.R
TODO.org
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/DEXSeq.R
inst/doc/DEXSeq.Rnw
inst/doc/DEXSeq.pdf
inst/python_scripts
inst/python_scripts/dexseq_count.py
inst/python_scripts/dexseq_prepare_annotation.py
man
man/DEXSeq-defunct.Rd
man/DEXSeq.Rd
man/DEXSeqDataSet.Rd
man/DEXSeqHTML.Rd
man/DEXSeqResults.Rd
man/accessors.Rd
man/counts.Rd
man/estimateDispersions.Rd
man/estimateExonFoldChanges.Rd
man/estimateSizeFactors.Rd
man/methods-gr.Rd
man/otherMethods.Rd
man/perGeneQValue.Rd
man/plotDEXSeq.Rd
man/plotDispEsts.Rd
man/plotMA.Rd
man/testForDEU.Rd
vignettes
vignettes/DEXSeq.Rnw
vignettes/DEXSeq.bib
DEXSeq documentation built on May 20, 2017, 10:08 p.m.