Man pages for acidgenomics/DESeqAnalysis
Acid Genomics DESeq2 Analysis Utilities
| alphaSummary | Alpha level cutoff summary statistics |
| alphaThreshold | Alpha threshold |
| apeglmResults | Run a quick pairwise contrast using lfcShrink with apeglm |
| base | Base methods |
| baseMeanThreshold | Base mean threshold |
| coerce | Coercion methods |
| combine | Combine multiple objects |
| contrastName | Contrast name |
| contrastSamples | Samples corresponding to a differential expression contrast |
| correlation | Correlation |
| deg | Differentially expressed genes |
| degIntersection | Intersection of differentially expressed genes |
| degPerContrast | Base mean threshold |
| 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 |
| DESeqAnalysis-package | DESeqAnalysis |
| deseqMinimal | Minimal DESeq2 example analysis |
| DESeqResultsList | List containing related DESeqResults objects |
| DESeqResultsList-class | List containing related DESeqResults objects |
| export | Export data from R |
| extract | Extract or replace parts of an object |
| importPairwiseContrasts | Import pairwise contrasts from a file |
| interestingGroups | Interesting groups |
| lfcShrink | Shrink log2 fold changes |
| lfcShrinkType | Shrunken log2 fold change (LFC) type |
| lfcThreshold | Log2 fold change threshold |
| markdownTables | Markdown tables |
| params | Shared parameter documentation |
| plotBaseMean | Plot base mean distribution |
| plotContrastScatter | Plot scatterplot of differential expression contrast |
| plotCounts | Plot counts |
| plotDegHeatmap | Differentially expressed gene heatmap |
| plotDegPca | Plot differentially expressed gene principal component... |
| plotDegStackedBar | Stacked bar plot of DEGs |
| plotDegUpset | UpSet plot of directional DEG intersections across contrasts |
| plotHeatmap | Heatmap |
| plotLfc | Plot log2 fold change distributions |
| plotMa | MA plot |
| plotPca | Principal component analysis plot |
| plotVolcano | Volcano plot |
| prepareTximportFiles | Prepare quant files for tximport |
| results | Results |
| resultsDiff | Relative difference of results |
| resultsMatrix | DESeq aggregate results matrix |
| resultsNames | Results names |
| resultsTables | Results tables |
| sampleData | Sample data |
| sanitizeTximportIdentifiers | Sanitize tximport identifiers |
| show | Show an object |
| transformType | Variance-stabilizing transformation type |
| updateObject | Update object |
