API for steinbaugh/DESeqAnalysis
Acid Genomics DESeq2 Analysis Utilities

Global functions
.alphaCol	Source code
.coerceResultsToList	Source code
.contrast2coef	Source code
.ddsMsg	Source code
.exportResultsMatrices	Source code
.exportResultsTables	Source code
.joinCounts	Source code
.joinRowData	Source code
.prepareResultsForPlot	Source code
.thresholdLabel	Source code
.transformCountsAxisLabel	Source code
.whichResults	Source code
DESeqAnalysis	Man page
DESeqAnalysis-class	Man page
DESeqAnalysis-package	Man page
DESeqAnalysisList	Man page
DESeqAnalysisList,SimpleList-method	Man page
DESeqAnalysisList,list-method	Man page
DESeqAnalysisList,missing-method	Man page
DESeqAnalysisList-class	Man page
DESeqResultsList	Man page
DESeqResultsList,DESeqAnalysis-method	Man page
DESeqResultsList,DESeqAnalysisList-method	Man page
DESeqResultsList,SimpleList-method	Man page
DESeqResultsList,list-method	Man page
DESeqResultsList,missing-method	Man page
DESeqResultsList-class	Man page
[,DESeqAnalysis,ANY,ANY,ANY-method	Man page
alphaSummary	Man page
alphaSummary,DESeqAnalysis-method	Man page
alphaSummary,DESeqDataSet-method	Man page
alphaThreshold	Man page
alphaThreshold,DESeqAnalysis-method	Man page
alphaThreshold,DESeqAnalysisList-method	Man page
alphaThreshold,DESeqResults-method	Man page
alphaThreshold,DESeqResultsList-method	Man page
alphaThreshold<-	Man page
alphaThreshold<-,DESeqAnalysis,NULL-method	Man page
alphaThreshold<-,DESeqAnalysis,numeric-method	Man page
alphaThreshold<-,DESeqAnalysisList,NULL-method	Man page
alphaThreshold<-,DESeqAnalysisList,numeric-method	Man page
alphaThreshold<-,DESeqResults,numeric-method	Man page
alphaThreshold<-,DESeqResultsList,NULL-method	Man page
alphaThreshold<-,DESeqResultsList,numeric-method	Man page
apeglmResults	Man page
apeglmResults,DESeqDataSet-method	Man page
as.DESeqDataSet	Man page
as.DESeqDataSet,DESeqAnalysis-method	Man page
as.DESeqTransform	Man page
as.DESeqTransform,DESeqAnalysis-method	Man page
base	Man page
baseMeanThreshold	Man page
baseMeanThreshold,DESeqAnalysis-method	Man page
baseMeanThreshold,DESeqAnalysisList-method	Man page
baseMeanThreshold,DESeqResults-method	Man page
baseMeanThreshold,DESeqResultsList-method	Man page
baseMeanThreshold<-	Man page
baseMeanThreshold<-,DESeqAnalysis,NULL-method	Man page
baseMeanThreshold<-,DESeqAnalysis,numeric-method	Man page
baseMeanThreshold<-,DESeqAnalysisList,NULL-method	Man page
baseMeanThreshold<-,DESeqAnalysisList,numeric-method	Man page
baseMeanThreshold<-,DESeqResults,NULL-method	Man page
baseMeanThreshold<-,DESeqResults,numeric-method	Man page
baseMeanThreshold<-,DESeqResultsList,NULL-method	Man page
baseMeanThreshold<-,DESeqResultsList,numeric-method	Man page
coerce	Man page
coerce,DESeqAnalysis,DESeqDataSet-method	Man page
coerce,DESeqAnalysis,DESeqResultsList-method	Man page
coerce,DESeqAnalysis,DESeqTransform-method	Man page
colnames,DESeqAnalysis-method	Man page
combine	Man page
combine,DESeqAnalysis,DESeqAnalysis-method	Man page
contrastName	Man page
contrastName,DESeqAnalysis-method	Man page
contrastName,DESeqResults-method	Man page
contrastName<-	Man page
contrastName<-,DESeqResults,character-method	Man page
contrastSamples	Man page
contrastSamples,DESeqAnalysis-method	Man page
correlation	Man page
correlation,DESeqAnalysis,missingOrNULL-method	Man page
correlation,DESeqResults,DESeqResults-method	Man page
deg	Man page
deg,DESeqAnalysis-method	Man page
deg,DESeqResults-method	Man page
degIntersection	Man page
degIntersection,DESeqAnalysis-method	Man page
degIntersection,DESeqAnalysisList-method	Man page
degIntersection,DESeqResultsList-method	Man page
degPerContrast	Man page
degPerContrast,DESeqAnalysis-method	Man page
deseq	Man page
deseqMinimal	Man page
dim,DESeqAnalysis-method	Man page
dimnames,DESeqAnalysis-method	Man page
export	Man page
export,DESeqAnalysis,character-method	Man page
export,DESeqDataSet,character-method	Man page
extract	Man page
importPairwiseContrasts	Man page Source code
interestingGroups	Man page
interestingGroups,DESeqAnalysis-method	Man page
interestingGroups<-	Man page
interestingGroups<-,DESeqAnalysis,NULL-method	Man page
interestingGroups<-,DESeqAnalysis,character-method	Man page
lfcShrink	Man page
lfcShrink,DESeqAnalysis-method	Man page
lfcShrink,DESeqAnalysisList-method	Man page
lfcShrink,DESeqDataSet-method	Man page
lfcShrink<-	Man page
lfcShrink<-,DESeqAnalysis,logical-method	Man page
lfcShrink<-,DESeqAnalysisList,logical-method	Man page
lfcShrinkType	Man page
lfcShrinkType,DESeqAnalysis-method	Man page
lfcShrinkType,DESeqAnalysisList-method	Man page
lfcShrinkType,DESeqResults-method	Man page
lfcShrinkType,DESeqResultsList-method	Man page
lfcThreshold	Man page
lfcThreshold,DESeqAnalysis-method	Man page
lfcThreshold,DESeqAnalysisList-method	Man page
lfcThreshold,DESeqResults-method	Man page
lfcThreshold,DESeqResultsList-method	Man page
lfcThreshold<-	Man page
lfcThreshold<-,DESeqAnalysis,NULL-method	Man page
lfcThreshold<-,DESeqAnalysis,numeric-method	Man page
lfcThreshold<-,DESeqAnalysisList,NULL-method	Man page
lfcThreshold<-,DESeqAnalysisList,numeric-method	Man page
lfcThreshold<-,DESeqResults,numeric-method	Man page
lfcThreshold<-,DESeqResultsList,numeric-method	Man page
markdownTables	Man page
markdownTables,DESeqAnalysis-method	Man page
markdownTables,DESeqResults-method	Man page
markdownTables,DFrameList-method	Man page
names,DESeqAnalysis-method	Man page
params	Man page
plotBaseMean	Man page
plotBaseMean,DESeqAnalysis-method	Man page
plotBaseMean,DESeqDataSet-method	Man page
plotBaseMean,DESeqResults-method	Man page
plotContrastScatter	Man page
plotContrastScatter,DESeqAnalysis-method	Man page
plotCorrelationHeatmap	Man page
plotCorrelationHeatmap,DESeqAnalysis-method	Man page
plotCounts	Man page
plotCounts,DESeqAnalysis-method	Man page
plotCounts,DESeqDataSet-method	Man page
plotCounts,DESeqTransform-method	Man page
plotDegHeatmap	Man page
plotDegHeatmap,DESeqAnalysis-method	Man page
plotDegHeatmap,DESeqResults-method	Man page
plotDegPca	Man page
plotDegPca,DESeqAnalysis-method	Man page
plotDegPca,DESeqResults-method	Man page
plotDegStackedBar	Man page
plotDegStackedBar,DESeqAnalysis-method	Man page
plotDegUpset	Man page
plotDegUpset,DESeqAnalysis-method	Man page
plotHeatmap	Man page
plotHeatmap,DESeqAnalysis-method	Man page
plotLfc	Man page
plotLfc,DESeqAnalysis-method	Man page
plotMa	Man page
plotMa,DESeqAnalysis-method	Man page
plotMa,DESeqResults-method	Man page
plotPca	Man page
plotPca,DESeqAnalysis-method	Man page
plotQuantileHeatmap	Man page
plotQuantileHeatmap,DESeqAnalysis-method	Man page
plotVolcano	Man page
plotVolcano,DESeqAnalysis-method	Man page
plotVolcano,DESeqResults-method	Man page
prepareTximportFiles	Man page Source code
results	Man page
results,DESeqAnalysis-method	Man page
results,DESeqDataSet-method	Man page
resultsDiff	Man page
resultsDiff,DESeqAnalysis,missingOrNULL-method	Man page
resultsDiff,DESeqResults,DESeqResults-method	Man page
resultsMatrix	Man page
resultsMatrix,DESeqAnalysis-method	Man page
resultsMatrix,DESeqAnalysisList-method	Man page
resultsNames	Man page
resultsNames,DESeqAnalysis-method	Man page
resultsNames,DESeqAnalysisList-method	Man page
resultsNames,DESeqDataSet-method	Man page
resultsNames,DESeqResultsList-method	Man page
resultsNames<-	Man page
resultsNames<-,DESeqAnalysis,character-method	Man page
resultsNames<-,DESeqResultsList,character-method	Man page
resultsTables	Man page
resultsTables,DESeqAnalysis-method	Man page
resultsTables,DESeqResults-method	Man page
rownames,DESeqAnalysis-method	Man page
sampleData	Man page
sampleData,DESeqAnalysis-method	Man page
sanitizeTximportIdentifiers	Man page Source code
show	Man page
show,DESeqAnalysis-method	Man page
transformType	Man page
transformType,DESeqAnalysis-method	Man page
transformType,DESeqAnalysisList-method	Man page
transformType,DESeqTransform-method	Man page
updateObject	Man page
updateObject,DESeqAnalysis-method	Man page