buildExonCountSet |
This functions are deprecated and will become defunct. |
buildExonCountSet-deprecated |
This functions are deprecated and will become defunct. |
constructModelFrame |
This functions are deprecated and will become defunct. |
constructModelFrame-deprecated |
This functions are deprecated and will become defunct. |
countReadsForDEXSeq |
This functions are defunct and will be deleted |
countReadsForDEXSeq-defunct |
This functions are defunct and will be deleted |
counts |
Accessors for the 'counts' slot of a DEXSeqResults object. |
counts,ExonCountSet-method,deprecated |
Accessors for the 'counts' slot of a DEXSeqResults object. |
counts-method |
Accessors for the 'counts' slot of a DEXSeqResults object. |
countTableForGene |
This functions are deprecated and will become defunct. |
countTableForGene-deprecated |
This functions are deprecated and will become defunct. |
design,ExonCountSet |
This functions are deprecated and will become defunct. |
design,ExonCountSet-deprecated |
This functions are deprecated and will become defunct. |
DEUresultTable |
This functions are deprecated and will become defunct. |
DEUresultTable-deprecated |
This functions are deprecated and will become defunct. |
DEXSeq |
Performs the differential exon usage test in a single command |
DEXSeq-defunct |
This functions are defunct and will be deleted |
DEXSeq-deprecated |
This functions are deprecated and will become defunct. |
DEXSeqDataSet |
DEXSeqDataSet object and constructors |
DEXSeqDataSet-class |
DEXSeqDataSet object and constructors |
DEXSeqDataSetFromHTSeq |
DEXSeqDataSet object and constructors |
DEXSeqDataSetFromSE |
DEXSeqDataSet object and constructors |
DEXSeqHTML |
DEXSeq HTML report writer |
DEXSeqResults |
DEXSeqResults object |
DEXSeqResults-class |
DEXSeqResults object |
doCompleteDEUAnalysis |
This functions are deprecated and will become defunct. |
doCompleteDEUAnalysis-deprecated |
This functions are deprecated and will become defunct. |
estimateDispersions |
Estimate the dispersions for a DEXSeqDataSet |
estimateDispersions,ExonCountSet-method-deprecated |
Estimate the dispersions for a DEXSeqDataSet |
estimateDispersions-method |
Estimate the dispersions for a DEXSeqDataSet |
estimateDispersions_BM |
This functions are deprecated and will become defunct. |
estimateDispersions_BM-deprecated |
This functions are deprecated and will become defunct. |
estimateExonDispersion |
This functions are deprecated and will become defunct. |
estimateExonDispersion-deprecated |
This functions are deprecated and will become defunct. |
estimateExonDispersionsForModelFrame_BM |
This functions are deprecated and will become defunct. |
estimateExonDispersionsForModelFrame_BM-deprecated |
This functions are deprecated and will become defunct. |
estimateExonFoldChanges |
Estimates exon usage coefficients from the fitted terms of the GLM. |
estimatelog2FoldChanges |
This functions are deprecated and will become defunct. |
estimatelog2FoldChanges-deprecated |
This functions are deprecated and will become defunct. |
estimateSizeFactors |
Estimate the size factors for a DEXSeqDataSet |
estimateSizeFactors,ExonCountSet-method,deprecated |
Estimate the size factors for a DEXSeqDataSet |
estimateSizeFactors-method |
Estimate the size factors for a DEXSeqDataSet |
ExonCountSet |
This class has been deprecated and will become defunct. |
ExonCountSet-class |
This class has been deprecated and will become defunct. |
exonIDs |
Accessor functions for DEXSeqDataSet details |
exonIDs<- |
Accessor functions for DEXSeqDataSet details |
featureCounts |
Accessor functions for DEXSeqDataSet details |
featureIDs |
Accessor functions for DEXSeqDataSet details |
featureIDs<- |
Accessor functions for DEXSeqDataSet details |
findOverlaps |
Methods from GRanges overlaps for the DEXSeq object |
findOverlaps-method |
Methods from GRanges overlaps for the DEXSeq object |
findOverlaps-methods |
Methods from GRanges overlaps for the DEXSeq object |
fitDispersionFunction |
This functions are deprecated and will become defunct. |
fitDispersionFunction-deprecated |
This functions are deprecated and will become defunct. |
geneCountTable |
This functions are deprecated and will become defunct. |
geneCountTable-deprecated |
This functions are deprecated and will become defunct. |
geneIDs |
Accessor functions for DEXSeqDataSet details |
geneIDs<- |
Accessor functions for DEXSeqDataSet details |
getCountVector |
This functions are deprecated and will become defunct. |
getCountVector-deprecated |
This functions are deprecated and will become defunct. |
groupIDs |
Accessor functions for DEXSeqDataSet details |
groupIDs<- |
Accessor functions for DEXSeqDataSet details |
makeCompleteDEUAnalysis_BM |
This functions are deprecated and will become defunct. |
makeCompleteDEUAnalysis_BM-deprecated |
This functions are deprecated and will become defunct. |
modelFrameForGene |
This functions are deprecated and will become defunct. |
modelFrameForGene-deprecated |
This functions are deprecated and will become defunct. |
newExonCountSet |
This functions are deprecated and will become defunct. |
newExonCountSet-deprecated |
This functions are deprecated and will become defunct. |
perGeneQValue |
Summarize per-exon p-values into per-gene q-values. |
plotDEXSeq |
Visualization of the per gene DEXSeq results. |
plotDispEsts |
Plot dispersion estimates |
plotDispEsts,ExonCountSet-method,deprecated |
Deprecated methods for ExonCountSet object |
plotDispEsts-method |
Deprecated methods for ExonCountSet object |
plotDispEsts-method |
Plot dispersion estimates |
plotMA |
Generate an MA plot |
plotMA,ExonCountSet |
Deprecated methods for ExonCountSet object |
plotMA,ExonCountSet-deprecated |
Deprecated methods for ExonCountSet object |
plotMA,ExonCountSet-method,deprecated |
Generate an MA plot |
plotMA-method |
Generate an MA plot |
plotMA-methods |
Generate an MA plot |
prepareAnnotationForDEXSeq |
This functions are defunct and will be deleted |
prepareAnnotationForDEXSeq-defunct |
This functions are defunct and will be deleted |
read.HTSeqCounts |
This functions are deprecated and will become defunct. |
read.HTSeqCounts-deprecated |
This functions are deprecated and will become defunct. |
sampleAnnotation |
Accessor functions for DEXSeqDataSet details |
sizeFactors,ExonCountSet-method,deprecated |
Deprecated methods for ExonCountSet object |
sizeFactors-method |
Deprecated methods for ExonCountSet object |
subsetByGenes |
This functions are deprecated and will become defunct. |
subsetByGenes-deprecated |
This functions are deprecated and will become defunct. |
subsetByOverlaps |
Methods from GRanges overlaps for the DEXSeq object |
subsetByOverlaps-method |
Methods from GRanges overlaps for the DEXSeq object |
subsetByOverlaps-methods |
Methods from GRanges overlaps for the DEXSeq object |
testExonForDEU |
This functions are deprecated and will become defunct. |
testExonForDEU-deprecated |
This functions are deprecated and will become defunct. |
testForDEU |
Test for Differential Exon Usage. |
testForDEU_BM |
This functions are deprecated and will become defunct. |
testForDEU_BM-deprecated |
This functions are deprecated and will become defunct. |
testGeneForDEU_BM |
This functions are deprecated and will become defunct. |
testGeneForDEU_BM-deprecated |
This functions are deprecated and will become defunct. |