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| alphaSummary | Alpha level cutoff summary statistics |
| alphaSummary-method | Alpha level cutoff summary statistics |
| apeglmResults | Run a quick pairwise contrast using lfcShrink with apeglm |
| apeglmResults-method | Run a quick pairwise contrast using lfcShrink with apeglm |
| as | Force an object to belong to a class |
| coerce | Force an object to belong to a class |
| coerce-method | Force an object to belong to a class |
| contrastName | Contrast name |
| contrastName-method | Contrast name |
| contrastName<- | Contrast name |
| contrastName<--method | Contrast name |
| contrastNames | Results names |
| contrastNames-method | Results names |
| contrastNames<- | Results names |
| contrastNames<--method | Results names |
| contrastSamples | Samples corresponding to a differential expression contrast |
| contrastSamples-method | Samples corresponding to a differential expression contrast |
| correlation | Correlation |
| correlation-method | Correlation |
| deg | Differentially expressed genes |
| deg-method | Differentially expressed genes |
| deseq | DESeq2 example analysis |
| DESeqAnalysis | DESeq2 differential expression analysis |
| DESeqAnalysis-class | DESeq2 differential expression analysis |
| DESeqAnalysisList | List containing related DESeq2 analyses |
| DESeqAnalysisList-class | List containing related DESeq2 analyses |
| export | Export |
| export-method | Export |
| importPairwiseContrasts | Import pairwise contrasts from a file |
| lfcShrinkType | Shrunken log2 fold change (LFC) type |
| lfcShrinkType-method | Shrunken log2 fold change (LFC) type |
| markdown | Markdown |
| markdown-method | Markdown |
| matchMetadataToFiles | Match user metadata to file names used for tximport |
| plotBaseMean | Plot base mean distribution |
| plotBaseMean-method | Plot base mean distribution |
| plotCorrelationHeatmap | Heatmap |
| plotCorrelationHeatmap-method | Heatmap |
| plotCounts | Plot counts |
| plotCounts-method | Plot counts |
| plotDEGHeatmap | Differentially expressed gene heatmap |
| plotDEGHeatmap-method | Differentially expressed gene heatmap |
| plotDEGPCA | Plot differentially expressed gene principal component analysis |
| plotDEGPCA-method | Plot differentially expressed gene principal component analysis |
| plotDEGStackedBar | Stacked bar plot of DEGs |
| plotDEGStackedBar-method | Stacked bar plot of DEGs |
| plotDEGUpset | UpSet plot of directional DEG intersections across contrasts |
| plotDEGUpset-method | UpSet plot of directional DEG intersections across contrasts |
| plotHeatmap | Heatmap |
| plotHeatmap-method | Heatmap |
| plotMA | MA-plot: plot differences versus averages for high-throughput data |
| plotMA-method | MA-plot: plot differences versus averages for high-throughput data |
| plotMeanAverage | MA-plot: plot differences versus averages for high-throughput data |
| plotPCA | Principal component analysis plot |
| plotPCA-method | Principal component analysis plot |
| plotQuantileHeatmap | Heatmap |
| plotQuantileHeatmap-method | Heatmap |
| plotVolcano | Volcano plot |
| plotVolcano-method | Volcano plot |
| prepareTximportFiles | Prepare quant files for tximport |
| results | Results |
| results-method | Results |
| resultsMatrix | DESeq aggregate results matrix |
| resultsMatrix-method | DESeq aggregate results matrix |
| resultsNames | Results names |
| resultsNames-method | Results names |
| resultsNames<- | Results names |
| resultsNames<--method | Results names |
| resultsTables | Results tables |
| resultsTables-method | Results tables |
| sampleData | Sample data |
| sampleData-method | Sample data |
| show | Show an object |
| show-method | Show an object |
| topTables | Top tables |
| topTables-method | Top tables |
| transformType | Variance-stabilizing transformation type |
| transformType-method | Variance-stabilizing transformation type |
| updateObject | Update an object to its current class definition |
| updateObject-method | Update an object to its current class definition |