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| DESeq2-package | DESeq2 package for differential analysis of count data |
| coef | Extract a matrix of model coefficients/standard errors |
| coef.DESeqDataSet | Extract a matrix of model coefficients/standard errors |
| collapseReplicates | Collapse technical replicates in a RangedSummarizedExperiment or DESeqDataSet |
| 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 (a.k.a. Gamma-Poisson) distribution |
| DESeqDataSet | DESeqDataSet object and constructors |
| DESeqDataSet-class | DESeqDataSet object and constructors |
| DESeqDataSetFromHTSeqCount | DESeqDataSet object and constructors |
| DESeqDataSetFromMatrix | DESeqDataSet object and constructors |
| DESeqDataSetFromTximport | DESeqDataSet object and constructors |
| DESeqResults | DESeqResults object and constructor |
| DESeqResults-class | DESeqResults object and constructor |
| DESeqTransform | DESeqTransform object and constructor |
| DESeqTransform-class | DESeqTransform object and constructor |
| 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. |
| estimateBetaPriorVar | Steps for estimating the beta prior variance |
| 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 |
| estimateDispersionsPriorVar | Low-level functions to fit dispersion estimates |
| estimateMLEForBetaPriorVar | Steps for estimating the beta prior variance |
| 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. |
| fpkm | FPKM: fragments per kilobase per million mapped fragments |
| fpm | FPM: fragments per million mapped fragments |
| getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the count data |
| lfcShrink | Shrink log2 fold changes |
| 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. |
| normalizeGeneLength | Normalize for gene length |
| normTransform | Normalized counts transformation |
| plotCounts | Plot of normalized counts for a single gene |
| plotDispEsts | Plot dispersion estimates |
| plotDispEsts-method | Plot dispersion estimates |
| plotMA | MA-plot from base means and log fold changes |
| plotMA-method | MA-plot from base means and log fold changes |
| plotPCA | Sample PCA plot for transformed data |
| plotPCA-method | Sample PCA plot for transformed data |
| plotSparsity | Sparsity plot |
| priorInfo | Accessors for the 'priorInfo' slot of a DESeqResults object. |
| priorInfo-method | Accessors for the 'priorInfo' slot of a DESeqResults object. |
| priorInfo<- | Accessors for the 'priorInfo' slot of a DESeqResults object. |
| priorInfo<--method | Accessors for the 'priorInfo' slot of a DESeqResults object. |
| removeResults | Extract results from a DESeq analysis |
| replaceOutliers | Replace outliers with trimmed mean |
| replaceOutliersWithTrimmedMean | Replace outliers with trimmed mean |
| results | Extract results from a DESeq analysis |
| resultsNames | Extract results from a DESeq analysis |
| rlog | Apply a 'regularized log' transformation |
| rlogTransformation | Apply a 'regularized log' transformation |
| show | Show method for DESeqResults objects |
| show-method | Show method for DESeqResults objects |
| 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. |
| summary | Summarize DESeq results |
| summary.DESeqResults | Summarize DESeq results |
| unmix | Unmix samples using loss in a variance stabilized space |
| varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the count data |
| vst | Quickly estimate dispersion trend and apply a variance stabilizing transformation |