![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg){kind=small}
![[Top]](../../../doc/html/up.jpg){kind=small}
| counts | Accessors for the 'counts' slot of a DESeqDataSet object. |
| counts-method | Accessors for the 'counts' slot of a DESeqDataSet object. |
| counts<--method | Accessors for the 'counts' slot of a DESeqDataSet object. |
| DESeq | Differential expression analysis based on the negative binomial distribution |
| DESeqDataSet | DESeqDataSet object and constructors |
| DESeqDataSet-class | DESeqDataSet object and constructors |
| DESeqDataSetFromHTSeqCount | DESeqDataSet object and constructors |
| DESeqDataSetFromMatrix | DESeqDataSet object and constructors |
| design | Accessors for the 'design' slot of a DESeqDataSet object. |
| design-method | Accessors for the 'design' slot of a DESeqDataSet object. |
| design<--method | Accessors for the 'design' slot of a DESeqDataSet object. |
| dispersionFunction | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object. |
| dispersionFunction-method | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object. |
| dispersionFunction<- | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object. |
| dispersionFunction<--method | Accessors for the 'dispersionFunction' slot of a DESeqDataSet object. |
| dispersions | Accessor functions for the dispersion estimates in a DESeqDataSet object. |
| dispersions-method | Accessor functions for the dispersion estimates in a DESeqDataSet object. |
| dispersions<- | Accessor functions for the dispersion estimates in a DESeqDataSet object. |
| dispersions<--method | Accessor functions for the dispersion estimates in a DESeqDataSet object. |
| estimateDispersions | Estimate the dispersions for a DESeqDataSet |
| estimateDispersions-method | Estimate the dispersions for a DESeqDataSet |
| estimateDispersionsFit | Low-level functions to fit dispersion estimates |
| estimateDispersionsGeneEst | Low-level functions to fit dispersion estimates |
| estimateDispersionsMAP | Low-level functions to fit dispersion estimates |
| estimateSizeFactors | Estimate the size factors for a DESeqDataSet |
| estimateSizeFactors-method | Estimate the size factors for a DESeqDataSet |
| estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression. |
| getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the count data |
| makeExampleDESeqDataSet | Make a simulated DESeqDataSet |
| nbinomLRT | Likelihood ratio test (chi-squared test) for GLMs |
| nbinomWaldTest | Wald test for the GLM coefficients |
| normalizationFactors | Accessor functions for the normalization factors in a DESeqDataSet object. |
| normalizationFactors-method | Accessor functions for the normalization factors in a DESeqDataSet object. |
| normalizationFactors<- | Accessor functions for the normalization factors in a DESeqDataSet object. |
| normalizationFactors<--method | Accessor functions for the normalization factors in a DESeqDataSet object. |
| plotDispEsts | Plot dispersion estimates |
| plotMA | MA-plot from base means and log fold changes |
| plotPCA | Sample PCA plot from variance-stabilized data |
| removeResults | Extract results from a DESeq analysis |
| results | Extract results from a DESeq analysis |
| resultsNames | Extract results from a DESeq analysis |
| rlogData | Apply a 'regularized log' transformation |
| rlogTransformation | Apply a 'regularized log' transformation |
| sizeFactors | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object. |
| sizeFactors-method | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object. |
| sizeFactors<--method | Accessor functions for the 'sizeFactors' information in a DESeqDataSet object. |
| varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the count data |