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
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,missingOrNULL-method Man page
export,DESeqAnalysis,missingOrNULL,missingOrNULL-method Man page
export,DESeqDataSet,character,missingOrNULL-method Man page
export,DESeqDataSet,missingOrNULL,missingOrNULL-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,DataFrameList-method Man page
matchMetadataToFiles Man page Source code
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
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
steinbaugh/DESeqAnalysis documentation built on June 25, 2022, 7:29 a.m.