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 <email@example.com> and Alejandro Reyes <firstname.lastname@example.org>|
|Date of publication||None|
|Maintainer||Alejandro Reyes <email@example.com>|
|License||GPL (>= 3)|
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.