buildExonCountSet | Makes an ExonCountSet object from R objects. |
class:ExonCountSet | "ExonCountSet", a container for exon count data |
constructModelFrame | Returns the model frame of an exonCountSet object for the GLM fits. |
countReadsForDEXSeq | Prepare annotation transcriptDb object for DEXSeq. |
countReadsForDEXSeq-deprecated | Prepare annotation transcriptDb object for DEXSeq. |
counts | Accessors for the 'counts' slot of a ExonCountSet object. |
counts-method | Accessors for the 'counts' slot of a ExonCountSet object. |
counts<--method | Accessors for the 'counts' slot of a ExonCountSet object. |
countTableForGene | Count table for a given geneID. |
design | Accessor function for the design annotation from a ExonCountSet object. |
design-method | Accessor function for the design annotation from a ExonCountSet object. |
design<--method | Accessor function for the design annotation from a ExonCountSet object. |
DEUresultTable | Get a result table from the analysis workflow. |
DEXSeq-deprecated | This functions are deprecated and will become defunct. |
DEXSeqHTML | HTML report writer |
doCompleteDEUAnalysis | Perform complete differential exon usage analysis |
estimateDispersions | Estimate dispersions |
estimateDispersions-method | Estimate dispersions |
estimateDispersions_BM | Estimate exon dispersions, using the deprecated "big model" method |
estimateExonDispersionsForModelFrame_BM | Estimates exon dispersions for the (deprecated) "big model" method |
estimatelog2FoldChanges | Fold changes (log2) from the fitted expression values in the GLM. |
estimateSizeFactors | Estimate the size factors for an ExonCountSet |
estimateSizeFactors-method | Estimate the size factors for an ExonCountSet |
ExonCountSet | "ExonCountSet", a container for exon count data |
ExonCountSet-class | "ExonCountSet", a container for exon count data |
exonIDs | Accessor for the exonIDs in an ExonCountSet object. |
exonIDs<- | Accessor for the exonIDs in an ExonCountSet object. |
fitDispersionFunction | Fit the mean-variance function. |
geneCountTable | Makes a count table for genes. |
geneIDs | Accessor for the geneIDs in an ExonCountSet object. |
geneIDs<- | Accessor for the geneIDs in an ExonCountSet object. |
makeCompleteDEUAnalysis_BM | Complete differential exon usage analysis |
modelFrameForGene | Makes the model frame for a geneID. |
newExonCountSet | Creates an ExonCountSet object |
perGeneQValue | Summarize per-exon p-values into per-gene q-values. |
plotDEXSeq | Visualization of the fitted expression, fitted splicing or the normalized counts. |
plotDispEsts | Diagnostic plot for dispersion estimates and dispersion fit |
plotDispEsts-method | Diagnostic plot for dispersion estimates and dispersion fit |
plotDispEsts-methods | Diagnostic plot for dispersion estimates and dispersion fit |
plotMA | Generate an MA plot |
plotMA-method | Generate an MA plot |
plotMA-methods | Generate an MA plot |
prepareAnnotationForDEXSeq | Prepare annotation transcriptDb object for DEXSeq. |
prepareAnnotationForDEXSeq-deprecated | Prepare annotation transcriptDb object for DEXSeq. |
read.HTSeqCounts | Read counts output from HTSeq script. |
sizeFactors | Accessor functions for the sizeFactors information in a ExonCountSet |
sizeFactors-method | Accessor functions for the sizeFactors information in a ExonCountSet |
sizeFactors<--method | Accessor functions for the sizeFactors information in a ExonCountSet |
subsetByGenes | Making an ExonCountSet object from another one with a subset of its genes. |
testForDEU | Test for Differential Exon Usage. |
testForDEU_BM | Test for Differential Exon Usage (with the old, deprecated "big model" approach. |
testGeneForDEU_BM | Test a single gene for differential exon usage using the old (and deprecated) "big model" approach. |
[-method | "ExonCountSet", a container for exon count data |