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.

Author
Simon Anders <sanders@fs.tum.de> and Alejandro Reyes <alejandro.reyes@embl.de>
Date of publication
None
Maintainer
Alejandro Reyes <alejandro.reyes@embl.de>
License
GPL (>= 3)
Version
1.20.1
URLs

View on Bioconductor

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.

Files in this package

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