Learn R Programming

DEXSeq (version 1.18.4)

Inference of differential exon usage in RNA-Seq

Description

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.

Copy Link

Version

Version

1.18.4

License

GPL (>= 3)

Maintainer

Alejandro Reyes

Last Published

February 15th, 2017

Functions in DEXSeq (1.18.4)

DEXSeq

Performs the differential exon usage test in a single command
DEXSeqHTML

DEXSeq HTML report writer
DEXSeq-defunct

This functions are deprecated and will become defunct.
counts

Accessors for the 'counts' slot of a DEXSeqResults object.
estimateExonFoldChanges

Estimates exon usage coefficients from the fitted terms of the GLM.
plotDEXSeq

Visualization of the per gene DEXSeq results.
DEXSeqResults-class

DEXSeqResults object
findOverlaps

Methods from GRanges overlaps for the DEXSeq object
DEXSeqDataSet-methods

Subset and replacements of DEXSeqDataSet slots
estimateSizeFactors

Estimate the size factors for a DEXSeqDataSet
DEXSeqDataSet-class

DEXSeqDataSet object and constructors
perGeneQValue

Summarize per-exon p-values into per-gene q-values.
featureCounts

Accessor functions for DEXSeqDataSet details
plotDispEsts

Plot dispersion estimates
testForDEU

Test for Differential Exon Usage.
plotMA-methods

Generate an MA plot
estimateDispersions

Estimate the dispersions for a DEXSeqDataSet